A method for manufacturing MOS transistor with hybrid hard mask includes providing a substrate having a dielectric layer and a polysilicon layer thereon, forming a hybrid hard mask having a middle hard mask and a spacer hard mask covering sidewalls of the middle hard mask on the polysilicon layer, performing a first etching process to etch the polysilicon layer and the dielectric layer through the hybrid hard mask to form a gate structure, performing a second etching process to form recesses in the substrate at two sides of the gate structure, and performing a SEG process to form epitaxial silicon layers in each recess.