The invention discloses an MMC topological structure based hybrid energy storage system which comprises a plurality of chemical energy storage batteries, a plurality of capacitors and an MMC topological structure based converter. Each chemical energy storage battery and each capacitor are connected with the converter through submodules, and one end of each submodule is connected with the corresponding chemical energy storage battery or the corresponding capacitor while the other end of each submodule is serially connected in the converter. Preferably, each submodule is a half-bridge submodule consisting of two fully-controlled power components and a capacitor, wherein the two fully-controlled power components are connected serially and then parallelly connected with the capacitor. More preferably, each submodule is a full-bridge submodule consisting of four fully-controlled power components and a capacitor, wherein the four fully-controlled power components are connected serially pairwise and then parallelly connected with the capacitor. The direct-current converter is simple in structure and convenient to expand, low-frequency isolation transformers are not needed, power control of a single energy storage unit can be realized by means of a simple control method, and reliability and redundancy of the whole energy storage system are improved.