Trump, who didn't mention Whitmer's name, complained about the governor's locking down certain areas during the coronavirus pandemic.
Multiple times during the event, crowds began to chant "lock her up, lock her up" repeating the phrase used during Trump's 2016 campaign stumping when he would bring up "Crooked Hillary" Clinton.
"You gotta get your governor to open up your state, OK?" Trump said, as his crowds began to chant.
Whitmer's emergency lockdown declarations have provoked lawsuits and a takeover at the state capitol building by armed protestors. Initially, Detroit had one of the highest rates of COVID-19 in the country with a high of 428 daily cases in April, and has seen more than 1,500 deaths.
The state has seen an increase in cases to more than 2,200 per day with 15 deaths reported Friday, according to the Johns Hopkins COVID-19 tracker. The positivity rate is 3.74%.
Trump referred to Whitmer's emergency orders as a "draconian unscientific lockdown" that keeps Michigan "locked up and locked down and closed for business."
Whitmer was also recently the target of a domestic terrorist plot, foiled by the FBI, to kidnap her, allegedly hold her on a "trial" on Nov. 3 and murder her and other state government officials, including Democratic Virginia Gov. Ralph Northam.
Fourteen people have been charged with state and federal crimes. Federal agents said political rhetoric contributed to the actions of the defendants.
As the crowd continued to chant "lock her up" again, Trump acknowledged that Whitmer had been in danger.
"Look, she said she was threatened," Trump said. "And she blamed me. And our people are the ones that worked with her people, so let's see what happens," he added.
Trump also complained during the rally about Whitmer's lack of gratitude to the federal government for supplies and PPE during the first wave of the pandemic.
"She'd go out and badmouth me," Trump said. "Hopefully you'll be sending her packing pretty soon." At that, the crowd began chanting again.
Trump's speech also attacked his traditional campaign stump speech opponents "sleepy Joe" Biden, CNN, social media companies and the "radical leftist agenda."
"The modern left does not use reason or persuasion to advance their cause. They use intimidation, coercion and control, and worse," Trump said. "They demand absolute allegiance or else ... and they want to cancel our entire heritage."
In a newer twist, Trump tried to evoke fear in the crowd by insisting that his opponent Joe Biden would "flood your great state with immigrants and refugees from terrorist hotspots all around the world."
He said Biden had a plan that would "turn Michigan into a refugee camp" and "overwhelm" the state with "poorly vetted migrants from jihadist regions."
The speech lasted more than an hour and Trump, at times, appeared to have a raspy voice after non-stop campaign appearances in Florida, Pennsylvania, Georgia, Iowa and South Carolina as he recovers from treatment for COVID-19.
The president gave a shoutout to Michigan conservative electric guitarist Ted Nugent and Republican National Committee Chair Ronna McDaniel, who is also recovering from COVID-19.
The weather in Muskegon was chilly with temperatures in the mid-40s and windy. Trump called for a hat several times during his speech, which was finally provided by a staffer.
Watch Trump's Michigan rally here: