A method is provided for fabricating a pixel structure of a CMOS transistor. The method includes providing a semiconductor substrate doped with first type doping ions; and forming a trench in the semiconductor substrate by etching the semiconductor substrate. The method also includes forming isolation layers on side surfaces of the trench to prevent dark current from laterally transferring; and forming an epitaxial layer doped with second type doping ions with a doping type opposite to a doping type of the first type doping ions in the trench. Further, the method includes forming a pinning layer on a top surface of the epitaxial layer; and forming a gate structure on a surface of the semiconductor substrate at one side of the epitaxial layer. Further, the method also includes forming a floating diffusion region in the semiconductor substrate at one side of the gate structure far from the epitaxial layer.