McKellar cited irreconcilable differences for the breakup from composer Michael Verta in her petition, which was filed on Monday in Los Angeles.
The 37-year-old is best known for playing Winnie Cooper on ABC's "The Wonder Years." She went on to author three books on mathematics with titles such as "Math Doesn't Suck" and "Kiss My Math."
The pair married in March 2009 and have a son who will be 2-years-old in September.
McKellar, who appeared in several episodes of "The West Wing" and other series, is seeking joint custody.
Her filing states the couple has a prenuptial agreement.