Disclosed is a harmonic control method for a photovoltaic power generation system. The method compensates a photovoltaic grid connected harmonic wave by the aid of a compensation reactor and an FC (fiber channel) filtration wave, influencing factors of a direct-current power supply of a photovoltaic array on the harmonic wave are simultaneously considered, the harmonic wave of the photovoltaic grid connected power generation system can be accurately compensated, the reactive power Q1 outputted by an inverter unit controller is received by an SVC (static var compensator) controller, the SVC controller comprehensively considers parameters such as system bus voltage Us, system inlet wire current Is, circuit breaker switching-closing conditions of an FC device, reactive power compensation quantity is calculated, reactive power compensation is realized by controlling a trigger angle alpha, and the reactive power compensation quantity is outputted in a PI adjusting mode.