The present invention provides an energy storage system multi-target control method with the consideration of battery health and a system. The method comprises the steps of (1) obtaining the parameter of an energy storage system, (2) determining an energy storage system power output target value which satisfies a wind power prediction error, (3) determining the volatility of wind storage combined power output, (4) judging whether the volatility of the wind storage combined power output satisfies a wind power grid connection requirement or not, and if not, correcting the energy storage system power output target value. The system comprises a data obtainment module, a multi-target control module, a volatility calculation module and a correction module. According to the method and the system provided by the invention, under the premise of considering the battery health state, the multi-target control of raising the ability of wind power tracking plan power output and stabilizing wind power volatility can be realized, and thus the friendliness of the wind power generation is comprehensively improved.