A polymer battery separator with an interpenetrating network structure and a preparation method thereof are disclosed. A multilayer microporous separator includes a PVDF layer, and a PE-PVDF porous substrate located on a surface of the PVDF layer. Finger-like through holes with a pore size of 100-150 nm are distributed in the PVDF finger-like pore layer. An interpenetrating network structure with a pore size of 50-100 nm is distributed on an interface between the PVDF finger-like pore layer and the PE microporous layer. Micropores with a pore size of 20-50 nm are distributed in the PE microporous layer. The surface of the PVDF layer is covered with the PE-PVDF porous substrate, so that the multilayer microporous separator forms an interpenetrating network structure, which has improved thermal stability and high-temperature resistance.