In the 2016 campaign, Mr Trump pledged to bring all troops home from "endless wars" but this has been criticised by military commanders, defence leaders and even Republicans anxious about the consequences of abruptly abandoning partners on the ground.
"I want to thank Dr. Anderson, Admiral Kernan and Jen Stewart for their service to the nation and the Department", Miller said in a statement of the newly resigned officials, whose tenure marks an exodus of decades of defence experience.
A USA defense official told CNN Thursday that Alexis Ross has handed in her resignation, making her the third member of the Defense Department to exit the team in as many days and the latest in a growing number of agency officials to leave the Pentagon this week amid a rapidly escalating post-election overhaul.
"It is hard to overstate just how risky high-level turnover at the Department of Defense is during a period of presidential transition".
Representative Elissa Slotkin, who previously worked in the Pentagon under Obama, told The New York Times there are only a few reasons why Trump would fire Esper, and it wasn't because of any wrongdoings on Esper's part. It's going to be a real "yes man". And if that happens, he says, quote, "God help us".
Since early this year, the White House has been purging Pentagon officials who were deemed insufficiently loyal to the White House and installed those who can be trusted to carry out the president's wishes. Esper said that job should be left to the National Guard.
More recently, Esper was viewed by the White House as stalling on the president's efforts to remove troops from Afghanistan.
The abrupt changes sent reverberations through the Pentagon as nervous civilian and military staff waited for the next shoe to drop.
Mark Milley, Chief of Staff appointed by Trump more than a year ago, took advantage of Veterans Day on Wednesdayto reassure Americans that the military is there to defend democracy - not the political interests of any individual.
Milley, in an interview last month with NPR, dismissed such talk as "speculation".
They're apparently concerned about Trump "raising the specter of using active duty forces under the Insurrection Act against any future protests" or him "overriding" military advice and withdraw troops from Afghanistan. Their replacements all have a reputation for being Trump loyalists. James Anderson, the acting undersecretary of defence for policy, quit on Tuesday after clashing with the White House over its attempts to insert allies and controversial figures into top Pentagon positions, Politico reported.
"Kash Patel, now on the National Security Council staff, has been named by Acting Secretary Miller as his Chief of Staff", the Pentagon announced on Tuesday.
Patel worked as a top aide to Representative Devin Nunes, the pro-Trump Republican who chaired the House Intelligence Committee and now is its top minority member.
"Anthony Tata is an Islamophobic conspiracy theorist who is so unqualified and ill-suited for a senior defense position that his confirmation hearing was pulled". Multiple inquiries have failed to produce evidence supporting these claims.
Flournoy, who served in the Obama administration as secretary of defense policy, co-founded WestExec Advisors, a consulting group that counts defense companies among its clients. Cohen-Watnick has reportedly favored using the US intelligence community to undermine or oust Iran's government. Those claims were never proven.
"We strongly encourage you to reject the mistaken nominations of the Trump era; and, again, commit to appointing Secretaries of Defense with no prior ties to defense contractors", the lawmakers wrote.
Miller has hired retired Army Colonel Douglas Macgregor as a top adviser.