The invention provides a photoelectric tracking system vision measurement time-lag compensation method based on a generalized proportional-integral observer. According to the situation that vision measurement time-lag exits in a photoelectric tracking system, the influence of the measurement time-lag on the system is reduced through a feedback control method based on the improved generalized proportional-integral observer, and meanwhile suppression of kinematic uncertainties in the system is realized. The core of the method is to use the observer to estimate the states, uncertainties and uncertainty differences of the system at previous moments, then estimation values and a state space model of the system are utilized to calculate the state and uncertainty of the system at the current moment, and finally control input of the system is obtained according to estimation values of the state and uncertainty of the system at the current moment. Through the method, the adverse influence of the vision measurement time-lag on the system is weakened, the uncertainty suppression capability of the system is improved, and the tracking precision of the system is improved.