The invention provides an energy efficiency prediction method of a photovoltaic power generation system. The energy efficiency prediction method comprises: a photovoltaic power generation system is divided into a photovoltaic array assembly, a direct-current cable assembly, a photovoltaic combiner box assembly, and an inverter assembly, and an output power of the photovoltaic array assembly, a power loss of the direct-current cable assembly, a power loss of the photovoltaic combiner box assembly, and a power loss of the inverter assembly are calculated respectively; and according to the output power of the photovoltaic array assembly, the power loss of the direct-current cable assembly, the power loss of the photovoltaic combiner box assembly, and the power loss of the inverter assembly, the energy efficiency of the photovoltaic power generation system can be calculated. With the method, an energy efficiency prediction result can be provided for station building site selection for an inbuilt photovoltaic power station and can be used as a theoretical reference. For the photovoltaic power station working normally, the operation state estimation and fault diagnosis of the photovoltaic station can be realized based on comparison of monitoring data and theoretical calculation, thereby providing a basis for utilizing the energy generated by the photovoltaic array to the greatest extent.