The invention discloses a multi-template monodisperse active notoginsenoside molecular imprinted polymer and a preparation method thereof. The method comprises the following steps of mixing and dissolving template molecules and functional monomers into a pore-forming agent, performing uniform ultrasonic mixing to form a template molecule-functional monomer composite, adding an effective amount of initiator and an effective amount of cross-linking agent, and performing ultrasonic nitrogen introduction and sealing; placing a molecular imprinted polymer in a shaking incubator for polymerization reaction under the protection of nitrogen and thermal initiation; after the polymerization reaction is finished, eluting an obtained molecular imprinted polymer by using a methanol-glacial acetic acid to remove the template molecules, washing the molecular imprinted polymer to be neutral by using methanol, and performing vacuum drying to obtain the multi-template monodisperse active notoginsenoside molecular imprinted polymer. Prepared precipitated molecular imprinted polymer microspheres have the advantages of high monodispersity, uniform particle diameter, size controllability, simplicity in preparation, high yield and the like; damage to binding sites and imprinted cavities is reduced, and high affinity and high selectivity of the polymer to the template molecules are ensured.