For harmonic and reactive compensation of shunt active power filter (SAPF), the higher the DC link voltage is, the better comthepensation performance will be. However, higher SAPF DC voltage will cause bigger switching loss and switching noise, which is bad for the long-time running of SAPF. Thus, an optimal DC link voltage control strategy is proposed based on the equivalent energy model of three-phase three-wire system of SAPF. According to the reactive powers which is consisted in power grid and conpensated by SAPF, the compensated result would be better when the reactive power is near to zero in power grid side. Moreover the optimal DC link referent voltage is calculated to decrease switching loss and switching noise in the strategy. Simulation and experiment results validate the correctness of the theoretical analysis.