The shunt active power filter(SAPF) cannot compensate harmonic and reactive current completely when capacity is limited. Aiming at the problem, an adaptive harmonic compensation control method based on second order generalized integrator(SOGI) is proposed with calculating APF’s capacity strictly. SOGI is used to extract the harmonic currents as instruction current. RDFT algorithm is used to calculate the RMS of each harmonic component. According to the SAPF’s capacity, the selective harmonic components to compensate and the corresponding ratio is adjusted adaptively. The PI and repetitive compound control strategy is used to track the compensation current accurately. Simulation analysis and experiments show that the stated method has obvious superiority in control simplicity and capacity utilization of SAPF.