Timing jitter is one of the main factors that influence on the accuracy of time domain precision measurement. Timing jitter compensation is one of the problems people concern. Because of the flaws of median method, PDF deconvolution method and synthetic method, we put forward a new method for timing jitter compensation, which is called advanced median method. The theory of the advanced median method based on probability and statistics is analyzed, and the process of the advanced median method is summarized in this paper. Simulation and experiment show that compared with other methods, the new method could compensate timing jitter effectively.