The 19-year-old actor - who plays Jake on the CBS sitcom - hit out at the series in a video testimonial for the Forerunner Christian Church, referring to the show as "filth" and asking fans to stop watching.
However, Two and a Half Men filming is continuing as usual, according to the Los Angeles Times, with a CBS spokesman noting that Jones's character does not appear in every episode of the show's current tenth season.
Former Two and a Half Men star Charlie Sheen was famously fired from the comedy in March 2011 after publicly criticising showrunner Chuck Lorre.
Sheen was replaced by Ashton Kutcher, who now appears opposite original star Jon Cryer on the series.
New episodes of Two and a Half Men air on Thursdays on CBS and on Mondays on Comedy Central in the UK.
> Jon Cryer on Emmy win: 'I can't believe Two and a Half Men success'
> Charlie Sheen talks "winning" meltdown: 'I was in total denial'
Watch Angus T Jones urge fans to "stop watching" Two and a Half Men below: