The invention provides an AGC (Automatic Generation Control) method and system for making stored energy participate in secondary frequency modulation of a power grid. The AGC method for making the stored energy participate in secondary frequency modulation of the power grid comprises the following steps of generating a real-time area control error and a real-time area control command of the power grid according to a frequency deviation and a link line exchange power deviation of the power grid; utilizing the real-time area control command and a preset control logic to distribute the regulating variable of a battery energy storage system and the regulating variable of each frequency modulation set according to a control interval where the real-time area control error is located; determining a real-time charge state of the battery energy storage system according to the regulating variable of the battery energy storage system and an initial charge state thereof; and determining and outputting the actual regulating variable of the battery energy storage system according to the real-time charge state of the battery energy storage system and the minimum charge state and the maximum charge state of the battery energy storage system.