Harvard University became the leader of academia’s resistance to the Trump administration — and soaked in acclaim from the White House’s critics — when it refused a roster of intrusive demands and took the government to court last month.

Legal experts saw a strong case, built by a team of elite conservative lawyers, to win back billions of research dollars that the government had stripped away. Supporters cheered on Harvard’s unusually sharp public tone.

“Congratulations to Harvard for refusing to relinquish its constitutional rights to Trump’s authoritarianism,” Senator Bernie Sanders of Vermont wrote on social media last month.

But behind the scenes, several senior officials at Harvard and on its top governing board believe that the university is confronting a crisis that could last until President Trump is out of power, according to three people involved in the discussions. Even if Harvard’s legal case is successful, these officials say, the school will still face enormous troubles that may force the nation’s oldest and wealthiest university to rethink its identity and scale.

Any outcome seems likely to lead to significant cuts to Harvard’s research and work force and undermine its pre-eminence for years. Without its sprawling research apparatus, there is a fear that it could become more like a small, teaching-focused liberal arts college.

University leaders believe the only clear options are either working with Mr. Trump or somehow securing huge sums of money quickly, perhaps from private donors, the three people said. They spoke on the condition of anonymity because they had not been authorized to discuss school officials’ private deliberations.

The crosscurrents are unlike any that the university has faced in its modern history. For centuries, Harvard has cherished its independence, its swaggering pride and its record of academic excellence. But Mr. Trump has reveled in unleashing chaos that many believe will be difficult to contain as long as he sees the university as a target.

On Monday, the Trump administration intensified the clash and threatened to choke off grant money to Harvard indefinitely.

“They can make your life unpleasant, even if they’re violating the law and a court ultimately determines they’re violating the law,” said Samuel R. Bagenstos, who was general counsel of the Health and Human Services Department during the Biden administration.

Harvard declined to comment on Thursday. But the dean of the Faculty of Arts and Sciences, Harvard’s largest division, acknowledged the scale of the university’s problems during a faculty meeting this week.

“These federal actions have set in motion changes that will not be undone, at least not in the foreseeable future,” said the dean, Hopi E. Hoekstra, according to the campus newspaper, The Harvard Crimson.

“While Harvard is challenging the funding freeze in court, we can’t assume that resolution will be reached quickly, or, even if Harvard prevails, that the funds will be returned in full,” Dr. Hoekstra said.

Mr. Trump and the executive branch have immense leverage over the school. The education secretary, Linda McMahon, said on Monday that the federal government would stop issuing grants and contracts to Harvard going forward, or at least try. Harvard received about $687 million in federal research money during its 2024 fiscal year, making the federal government its largest revenue source for a portfolio of projects that range from tuberculosis to space travel research.

Harvard recently issued $750 million in bonds, and its endowment is valued at more than $53 billion. But most of the endowment money is restricted, meaning that it cannot be spent at will.

Harvard has already imposed a hiring freeze and started layoffs. Dean Hoekstra’s division has an internal group, now known as the Research Continuity Committee, studying how the university can use a far smaller pot of research money that does not come from the federal government.

For now, the Harvard Corporation, the board that oversees the university, has decided to stay the course and keep fighting. Board members are acutely sensitive to the uproar that followed when Columbia University and major law firms like Paul, Weiss cut deals with Mr. Trump, according to two of the three people involved in the discussions.

But some officials have wondered whether the school might face less blowback for a deal, since Harvard leaders could frame any agreement as a successful settlement to the muscular litigation they brought. That lawsuit was in response to a list of demands that the government sent in April, requiring the university to submit to new audits, alter its admissions and hiring practices, dilute faculty influence and establish “viewpoint diversity.”

The corporation has told the school’s lawyers not to engage with the Trump administration, according to the two people involved in discussions.

Complicating matters is whether the White House will honor a deal.

Lawrence H. Summers, a former Harvard president, said in an interview that it was difficult to judge any potential settlement before its terms became public. But, he said, “It would be a tragedy if Harvard resolved this in a way that gave support and encouragement to the idea of extralegal extortion.”

“Harvard is almost uniquely well positioned — much better than any individual law firm or any individual company or almost any other institution — to resist unlawful extortion because of its resources, because of its prestige, because of the breadth of its network,” he said.

The Trump administration has encouraged the university to negotiate. Harrison Fields, a White House spokesman, said last month that Harvard’s aggressive response to the administration’s demands was “showboating.” He added: “They know more than anyone that not playing ball is going to hurt their team.”

The Trump administration this week reiterated its aim to inflict as much damage as possible, when Ms. McMahon fired off a letter telling Harvard that it would not receive future federal grants. Although experts on government contracts and grants scoffed at the missive, the government can essentially blacklist contractors through a process called debarment.

Debarment is not an overnight procedure, and it can be challenged. But a victory for Harvard could be a hollow one since the Trump administration could still try to manipulate the grant-making process away from the school, academics said in interviews this week.

Dr. Daniel W. Jones, a former University of Mississippi chancellor who also led the medical school there, said federal agencies had substantial sway over funding decisions, even when peer review was involved.

“They could find a reason,” said Dr. Jones, a former president of the American Heart Association who often consults on grants. “So much has been turned upside down.”

Litigation can last months or years. Harvard is seeking a speedy end to its pending case against the government, but the next hearing is not until July. Appeals could extend the battle, too, stripping Harvard of money and time.

Dr. Jones has also noted that researchers “can’t just stop science and pick it back up.” Even if Harvard ultimately wins in court, funding disruptions could have already upended or compromised carefully structured projects.

“Harvard is in a really bad spot,” Mr. Bagenstos, the Biden official, said. All of higher education, he added, “is in a really bad spot here.”

Aside from the research funding, there will be nothing to stop the administration from saddling the school with more onerous and potentially costly investigations, like the ones currently being conducted by at least five different departments and agencies, including the Justice Department and Department of Homeland Security.

Some university officials fear those investigations, which so far appear to be only civil matters, could swell into full-blown criminal inquiries in the coming months.