The invention discloses a mesoporous molecular sieve SBA-15 composite nano surface imprinted polymer and a preparation method thereof. The preparation method comprises the following steps: dispersing mesoporous molecular sieve SBA-15 powder into a methylbenzene solution in an ultrasonic mode, further adding methylacryloyl acyloxy propyl triethoxy silane so as to prepare a modified mesoporous molecular sieve SBA-15, further washing by using methylbenzene and methanol in sequence in the ultrasonic mode, centrifuging, and finally drying in vacuum for later use; adding template molecules and functional monomers into a pore-foaming agent, and dissolving in the ultrasonic mode to prepare a pre-assembled solution A; dispersing the modified mesoporous molecular sieve into the pore-foaming agent so as to obtain a solution B; mixing the solutions, further adding a cross-linking agent and an initiating agent, and raising the temperature to perform polymerization reaction; and after the reaction, centrifuging to remove the supernate, repeatedly washing a product by using a methanol-glacial acetic acid mixture solution in the ultrasonic mode, and further washing by using methanol to be neutral so as to obtain the mesoporous molecular sieve SBA-15 composite nano surface imprinted polymer. Due to adoption of the polymer, high-efficient separation and purification of in-vivo baicalin are achieved.