The application relates to a hybrid energy storage output control method and system for stabilizing the peak-valley difference of a power grid, and aims at the problem that the expected value of charge and discharge power of a hybrid energy storage system does not consider the peak and valley of load. The method includes the following steps: first, the measured power of a hybrid energy storage system for peak load shifting is detected and collected in real time, and the expected value of charge and discharge power of the hybrid energy storage system is calculated by adopting a quadratic exponential smoothing algorithm and considering a peak-valley factor; and then, the output of a super capacitor and a lithium battery is determined according to the change of the expected value of charge and discharge power of the hybrid energy storage system, and is optimized by a global parallel optimization algorithm. The method of the invention combines the peak-valley factor, a variable-coefficientexponential peak load shifting method, a non-linear state observation method and the global parallel optimization algorithm, and provides effective reference for the capacity configuration of the energy storage system.