The invention discloses a channel MOS P-N junction Schottky diode structure and a manufacturing method thereof. The structure mainly comprises a substrate, a channel structure, a polysilicon layer, an oxide layer, a metal layer and an ion implantation area; and the manufacturing method comprises the following steps: providing the substrate; forming a first mask layer on the substrate; performing a first photoetching process to form the channel structure; growing a gate oxide layer in the channel structure; performing an ion implantation process to form the ion implantation area; forming the polysilicon layer in the channel structure; forming a second mask layer on partial polysilicon layer and the first mask layer; performing a second photoetching process to form a side wall structure andexpose the partial polysilicon layer and the substrate; and forming the metal layer on a generating structure. The channel MOS P-N junction Schottky diode structure has the characteristics of low reverse voltage leakage current, low forward voltage drop value, high reverse withstanding voltage value and low reverse recovery time.