The invention discloses a wind power plant storage capacity optimizing method taking battery service life and the over-discharge phenomenon into consideration. The method includes the following steps that firstly, according to work principles of an energy storage system, the minimum comprehensive economic cost of operation cost, penalty cost and inherent cost is taken as an optimization target, and a target function of energy storage capacity optimization is built; secondly, constraint conditions are built, wherein the constraint conditions include power constraint, capacity constraint and battery service life constraint; thirdly, according to the built target function and the constraint conditions, the optimal energy storage capacity is obtained by means of a genetic algorithm. According to the optimal capacity obtained through the method, low economic cost is guaranteed, and power fluctuation is controlled within a small range. Besides, the relation between the operation cost, the penalty cost and the inherent cost is analyzed, and necessity of introduction of the operation cost is proved.