The invention discloses a rectangular wave modulation method for a modular isolation type battery energy storage converter. According to the invention, the duty ratio of the alternating voltage at the primary and secondary sides of a transformer in a half switching cycle is less than 0.5, the direction and size of energy transfer between an energy storage battery and a direct-current power grid are controlled by adjusting the phase difference between the primary rectangular wave voltage and the secondary rectangular wave voltage, the direct-current bus capacitor voltage of each sub module of the bridge arm at the secondary side of the transformer is stabilized by correcting the phase difference, and the average of current at the secondary side of the transformer, namely, the direct-current distribution network current is adjusted by adjusting the direct-current component of the output voltage of all the sub modules of the bridge arm at the secondary side of the transformer. Therefore, the purpose of module voltage stabilizing and grid-connected current controlling is achieved, and stable and reliable operation of the system is realized.