The invention relates to a high-molecular organic polymer template synthesized compound pore structure molecular sieve and a preparation method thereof and belongs to the technical field of compound pore structure molecular sieve preparation. The technical scheme is that the preparation method comprises the following steps of: forming molecular sieve gel, wherein a certain amount of silicon source, aluminum source, template agent and deionized water are uniformly mixed under room temperature; and a certain amount of PEI (Polyethyleneimine) is added to the uniformly mixed molecular sieve gel as a mesoporous structure guide agent for being uniformly stirred; carrying out hydrothermal reaction, wherein the hydrothermal reaction temperature is 100 DEG C to 250 DEG C, the hydrothermal reaction is carried out directly or under stirring conditions and the reaction time is 12 hours to 168 hours; drying, wherein the drying is carried out for 6 hours to 48 hours under 50 DEG C to 150 DEG C; and roasting to obtain the molecular sieve with the compound pore structure, wherein the roasting is carried out for 1 hour to 24 hours under 300 DEG C to 800 DEG C.