The invention discloses a target tracking method and system based on mean shift in a complex scene. The method includes the steps of obtaining video data of the scene, performing moving target separation on the video data to obtain a foreground target, extracting second order color histogram features in the foreground target and gradient weighted histogram features in the foreground target, and using a mean shift algorithm as a frame for conducting target tracking on the foreground target on the basis of the second order color histogram features and the gradient weighted histogram features. According to the method, due to the fact that the second order color histogram features and the gradient weighted histogram features are integrated and the mean shift algorithm is used as the frame for achieving target tracking, and accuracy and robustness of the target tracking algorithm can be improved.