The invention discloses a method and a system for analyzing small interference probability stability of a wind power integration power system. The method comprises the following steps: generating random wind speed samples corresponding to various predetermined wind farms, and calculating random output sample sequences corresponding to the predetermined wind farms; reading original trend data files of the power system integrated with the predetermined wind farms, and determining original total output of the predetermined wind farms in the power system and original total output of conventional units; modifying the original outputs of the predetermined wind farms and the original outputs of the conventional units according to the random output sample sequences of the predetermined wind farms to obtain new trend data files; transferring a BPA small interference stability analysis program to carry out deterministic small interference stability analysis on the power system which is updated by the new trend data files; and counting the analysis results, and determining small interference stability probability indexes of the power system. Small interference probability analysis is carried out on the power system containing wind power to comprehensively analyze the influence of the wind power integration on the system.