The invention provides an adaptive control method and system for a battery energy storage systems connected in parallel, The method comprises, by calculating an initial target power of each battery energy storage system, Power Requirement Value of Power Grid, and determining the output increment of the battery energy storage system which distributes the initial target power of the battery system in the non-output state to the battery energy storage system in the incremental output state according to the working interval and the output state determined by the real-time charge state of the battery energy storage system, and finally determining the output reference value of each individual battery energy storage system. The invention realizes the adjustment of the charging and discharging state of the battery energy storage systems connected in parallel, Compared with the existing virtual synchronous machine technology, according to the difference of SOC between different battery energy storage units, the control strategy considering SOC is proposed, which effectively solves the problem of SOC unbalance among the battery energy storage systems connected in parallel, and avoids the overcharge and overdischarge of the energy storage system.