The invention discloses a method for correcting kinematic errors in a microscopic vision system, which is applied to the microscopic vision system. The method comprises the following steps of: calibrating a camera through a calibration board, establishing a camera model, tracking angular points of the calibration board, generating a tracking trajectory and an ideal revolving trajectory of the angular points through a least square method, then performing error evaluation, establishing an error correcting model, and correcting the microscopic image by virtue of the error correct model. The method provided by the invention can be used for establishing the error correct model for the microscopic vision system only through one-time error evaluation; and the model can be used for any microscopic movement video collected by the system, reducing the movement errors of the system and improving the three-dimensional reconstruction precision, thus being high in practicability.