The energy storage system consists of a large number of cells connected in series and parallel, and the inconsistency of the cells leads to a decrease in capacity utilization and system efficiency. In order to improve the granularity of system control, each modular battery is equipped with an isolated DC/DC converter, which adopts the architecture of parallel output between each module. In this paper, an isolated converter topology and its control method are proposed to realize the function of control the modular battery power flow. For the independent-input and parallel-output (IIPO) system, adaptive balancing control method is designed based on the balanced state of capacity(SOC) or current control objective, and verified by simulation. Finally, a 4.8kW prototype is built to verify the circuit design and control method.