Disclosed are a display apparatus, three-dimensional (3D) glasses and a control method thereof. The method of controlling three-dimensional (3D) glasses for a display apparatus includes: synchronizing clocks for communicating with the 3D glasses; generating drive timing information for driving shutters of the 3D glasses from the synchronized clocks and a frame sync signal of a displayed image; and transmitting a glasses control message, comprising the drive timing information, to the 3D glasses.