The president's provocation of Republican senators comes even though he will need their cooperation to pass key legislative items in the coming months. Upcoming measures include bills to raise the debt ceiling to avert default, fund the government to avoid a shutdown and overhaul the American tax system.
Tax reform, in particular, is an issue the president pressed for during his campaign, and he sees it as fundamental to boosting economic growth.
A New York Times report Tuesday described the president's deteriorating relationship with the GOP Senate leader in great detail. Trump and McConnell have not spoken in weeks, and the senator privately has been skeptical about whether Trump "will be able to salvage his administration," the Times reported.
McConnell "has fumed over Mr. Trump's regular threats against fellow Republicans and criticism of Senate rules," the newspaper said.
In a statement Wednesday, McConnell said he, Trump and both of their teams "have been and continue to be in regular contact about our shared goals." They are working together on issues like creating jobs, raising the debt ceiling, funding the government, and setting the defense budget, among other issues, the statement added.
"We have a lot of work ahead of us, and we are committed to advancing our shared agenda together and anyone who suggests otherwise is clearly not part of the conversation," the senator said.
Late Wednesday, the White House put out a statement saying that McConnell and Trump "remain united on many shared priorities, including middle class tax relief, strengthening the military, constructing a southern border wall, and other important issues."
Still, Trump's Arizona rally is not likely to make their relationship any better.
First, Trump called for Republicans to scrap the filibuster for legislation, which can be used to require that a measure needs 60 votes to pass. Trump has repeatedly slammed the rule, even though the GOP failed to get even 50 votes needed to repeal Obamacare under the budget reconciliation process.
"We have to," Trump said of removing the filibuster. "And if we don't, the Republicans will never get anything passed. You're wasting your time."
"We have to speak to Mitch, and we have to speak to everybody," the president added.
He reiterated the demand on Wednesday morning in a tweet.
Trump's veiled and direct attacks on McCain and Flake are also not likely to make his party's Senate leader any more friendly.
A super PAC that the Times described as "aligned with" McConnell recently released an ad critical of Kelli Ward, the Republican candidate challenging Flake in the GOP primary next year.
McConnell spokesman David Popp told CNBC that Republican senators have made it clear they don't want to change the rule.
The White House did not respond to a request for comment on this article.
The Trump-McConnell relationship and recent White House chaos have put one Trump Cabinet member in a particularly awkward spot. Transportation Secretary Elaine Chao is married to McConnell.
After Trump's widely criticized news conference last week responding to violence at a white nationalist rally in Charlottesville, Virginia, Chao said, "I stand by my man — both of them."