Miller, 41, has been one of Trump’s closest aides for more than a decade and is the president’s most powerful and hawkish voice on immigration. He also holds the title of homeland security adviser.
Trump announced the change on Friday as Wiles prepared to leave the job the same day.
Democrats have already signalled they will treat the appointment as a fight over the administration’s immigration record, including the Minneapolis shootings and the tactics used in raids.
Miller has been instrumental in driving the mass deportation programme during Trump’s second term, a campaign that has often featured violent raids by masked agents.
Miller’s dual role as homeland security adviser has tied him closely to the deportation drive that has defined much of the second term.
He faced particular criticism after immigration agents fatally shot two protesters in Minneapolis in January. Those incidents sparked mass demonstrations.
The top Democrat in the U.S. Senate vowed on Friday to vigorously oppose Miller’s appointment.
Wiles, 69, who recently said she had been given the all-clear from breast cancer, said in a statement on X that Friday would be her last day.