Two novel porous 2D covalent organic frameworks (COFs) with periodically heterogeneous pore structures were successfully synthesized through desymmetrized vertex design strategy. Condensation of C-2v, symmetric 5-(4-formylphenyl)isophthalaldehyde or 5-((4-formylphenyl)ethylene)isophthalaldehyde with linear hydrazine linker under the solvothermal or microwave heating conditions yields crystalline 2D COFs, HP-COF-1 and HP-COF-2, with high specific surface areas and dual pore structures. PXRD patterns and computer modeling study, together with pore size distribution analysis confirm that each of the resulting COFs exhibits two distinctively different hexagonal pores. The structures were characterized by FT-IR, solid state C-13 NMR, gas adsorption, SEM, TEM, and theoretical simulations. Such rational design and synthetic strategy provide new possibilities for preparing highly ordered porous polymers with heterogeneous pore structures.