When the grid connected PV(photovoltaic) power system supply faults occurred, the fault current of PV power happens transient, due to the protective effect of inverter control circuit, fault current is low, as the traditional detection methods don’t satisfy the requirements of grid connected PV generation. In order to seek protection for grid connected PV power system, the simulation model was set up based on PSCAD/EMTDC，the characteristics of the short-circuit current are analyzed, and Hilbert-Huang Transform(HHT) was proposed to decompose the fault waveform of current, which found the instantaneous frequency of the fault current is change when single-phase to groud fault occurs, with this the protection scheme of grid connected PV system based on HHT is proposed. The effective and feasible of this protection scheme is verified.