Astin was born on May 12, 1973, in Los Angeles, California, the son of actress Patty Duke and actor John Astin. His half-brother is actor Sean Astin. He attended Ralph Waldo Emerson Middle School and University High School in Los Angeles. He is married to Jennifer Abbott Astin (née Bautz).
Astin made his acting debut at age 9 in the TV movie Lois Gibbs and the Love Canal, but is probably best remembered for his television role as Andy Moffett over four seasons from 1985 to 1988 on the popular sitcom The Facts of Life. He has made guest appearances on Lost, House, Psych, Grey's Anatomy, Scandal, and NCIS. Astin has appeared in motion pictures including Iron Will, Wyatt Earp with Kevin Costner, The Evening Star with Shirley MacLaine, and Whit Stillman's The Last Days of Disco. During filming of The Evening Star, Mackenzie lost the top edge of his right ear in a car accident. In order to match scenes previously filmed, he was fitted with a prosthetic attachment to his ear for the remainder of the production. From 2005 to 2010, he worked with his father, the Director of the Program in Theatre Arts and Studies at Johns Hopkins University in Baltimore, Maryland.