A low gate charging rectifier having a MOS structure and a P-N junction and a manufacturing method thereof are provided. The low gate charging rectifier is a combination of an N-channel MOS structure and a lateral P-N junction diode. A portion of the gate-covering region is replaced by a thicker dielectric layer or a low conductivity polysilicon layer. In a forward mode, the N-channel MOS structure and the P-N junction diode are connected with each other in parallel. Under this circumstance, like the Schottky diode, the low gate charging rectifier has low forward voltage drop and rapid switching speed. Whereas, in a reverse mode, the leakage current is pinched off and the N-channel is shut off by the depletion region of the P-N junction diode, so that the low gate charging rectifier has low leakage current.