The invention discloses shutter glasses and a control system and method for controlling the shutter glasses. The control system comprises a receiver, a timer and a resetting device, wherein the receiver receives 3D starting signals and frame refreshing signals, the timer uses a high level moment of the 3D starting signals as an initial point and retimes every time when the positive source trigger of one frame refreshing signal is detected, and the resetting device resets the control signals of a left glass piece and a right glass piece at the moment when the positive source of the frame refreshing signal is triggered when the time of positive source triggering of the frame refreshing signal is larger than a preset value. A mechanism for detecting the 3D starting signals is added, when the 3D starting signals are detected to be in high level, the time of positive source triggering of the frame refreshing signal is calculated to be larger than the preset value or not, when the time is larger than the preset value, left and right eye control signal resetting is conducted on the shutter glasses, starting of the left glass piece and the right glass piece is made to be matched with an image signal of a left eye and an image signal of a right eye, the dislocation phenomenon of the shutter glasses can be effectively removed, and the fact that a user dizzies due to the dislocation phenomenon is reduced.