For the purpose of actual applications of large capacity active power filter（APF）， this paper proposes a control strategy to make three-phase three-wire APFs work in parallel. The APFs operate independently and have the capacity-maximum function of compensating load harmonics. Furthermore， the output current of the APFs is optimized up to capacity maximum， so that large capacity APFs compensate more， and small ones compensate less. In this way， the feasibility and security of paralleled running of APFs can be guaranteed. The control strategies for APFs’ switching is also proposed to ensure APFs switch corresponding to actual load harmonic currents and impact slightly to system. In the end， the simulation and experiment testify the validity of proportion compensation capacities based on capacity limit of APFs and the feasibility of coordination control strategy for parallel running of APFs.