Dott, 47, who won the world title in 2006, is accused of sexually assaulting a girl aged around 10 from 1993 to 1996, according to court papers.
He is also charged with sexual offences against a boy from 2006 to 2010, when the child was around eight years old.
"Graeme Dott has been suspended by the WPBSA due to a case which is scheduled to be heard before the High Court in Scotland," the World Professional Billiards and Snooker Association said in a statement.
"Whilst court proceedings are ongoing, it would be inappropriate for the WPBSA to make any further comment," it added.
A professional snooker player for nearly 30 years, Dott was a world championship runner-up in 2004 and 2010.
His suspension comes as he was set to enter this year's World Snooker Championship that kicked off this week in Sheffield, northern England.