The appointed investigator will review classified reports about the 2019 and 2021 federal elections and will make recommendations for future contests.
Rival political party leaders have called for a public inquiry.
China has denied any election interference, calling the claims "purely baseless and defamatory".
Speaking to reporters on Parliament Hill in Ottawa on Monday, Mr Trudeau said the reports challenging Canada's "sovereignty" are alarming, and "strike us to our very core as Canadians".
"I will be appointing an independent special rapporteur, who will have a wide mandate and make expert recommendations on combating interference and strengthening our democracy," Mr Trudeau said.
The rapporteur has not yet been chosen, he said, adding that the appointment will be made in the coming days.