The invention provides a power complementation control method and system for a hybrid energy storage system. The method includes the following steps that: the operation phase of a power grid is determined according to the compensation amount state of the power grid; and judgment is performed according to the compensation sequence of each energy storage system in the hybrid energy storage system and the magnitude of the compensation amount of the power grid, if the state of charge of the energy storage system of a first priority can satisfy the compensation amount of the power grid, the energystorage system of the first priority performs charging/discharging according to the operation phase of the power grid, otherwise, after the charging/discharging of the energy storage system of the first priority terminates, the energy storage system of a second priority performs supplementary charging/discharging. According to the power complementation control method and system for the hybrid energy storage system of the invention, the charging and discharging time sequence and power of a storage battery and a super capacitor are adjusted optimally on the basis of the complementary advantagesof the energy storage battery and the super capacitor, and therefore, grid connection power fluctuation can be effectively suppressed, and the loss of energy storage can be decreased.