The 49-year-old actor voiced his love for Aniston, 52, while discussing their 2017 split in the April/May issue of Esquire magazine.
Theroux and Aniston announced their split in February 2018 after two years of marriage.
"This decision was mutual and lovingly made at the end of last year," the pair said at the time. "We are two best friends who have decided to part ways as a couple, but look forward to continuing our cherished friendship."
In the Esquire interview, Theroux addressed rumors that he and Aniston split because he wanted to live in New York while Aniston wanted to live in Los Angeles.
"That's a narrative that is not true, for the most part," Theroux said. "Look, people create narratives that make themselves feel better or simplify things for them. That whole 'This person likes rock 'n' roll, that person likes jazz. Of course!' That's just not the case. It's an oversimplification."
Theroux confirmed he has remained friends with Aniston since their divorce, saying they don't talk every day but do call, FaceTime and text each other.
"Like it or not, we didn't have that dramatic split, and we still love each other," Theroux said. "I'm sincere when I say that I cherish our friendship. We can not be together and still bring each other joy and friendship."
"Also, she makes me laugh very, very hard. She's a hilarious person," he added. "It would be a loss if we weren't in contact, for me personally. And I'd like to think the same for her."
Theroux will next star in the Apple TV+ series The Mosquito Coast. The series is based on the novel of the same name by Theroux's uncle Paul Theroux, and co-stars Melissa George, Logan Polish and Gabriel Bateman.
Apple TV+ released a trailer for The Mosquito Coast this month that shows Theroux's character, Allie Fox, and his family on the run. The series will premiere April 30.