The 49-year-old man faces two counts of causing unnecessary pain, suffering or injury to an animal.
The society received a complaint from someone who said that an adult raccoon had been locked in a trap on a south Ottawa property for two days in June.
"Investigators arrived to a gruesome scene: the adult had a barbecue rotisserie rod shoved through its mouth and out the back of its head," the news release said. "The baby was found nearby, bludgeoned with a hammer.
"A veterinary exam found both animals suffered multiple wounds and had been alive through most of the ordeal."
If convicted, the man faces up to five years in jail and a lifetime ban on owning animals.
"We'll be recommending the maximum sentence," Ottawa Humane Society investigator Miriam Smith is quoted as saying.
"It's a severe case of abuse on two helpless animals."
The man is scheduled to make his first court appearance in October.