The invention discloses a method for preparing an organic-inorganic compound mesoporous film and application thereof, and belongs to the field of film materials. The preparation method comprises three steps of preparing precursor liquid, synthesizing a compound mesoporous film by using microwaves and eluting an surface active agent in the film, wherein the inorganic meso-porous material is assembled in pores in the polycarbonate film by the microwave synthesis to prepare the compound film, and the surface active agent in the compound film is removed by an extraction elution method, so that one or more organic-inorganic compound mesoporous films are obtained. The pore diameter of the mesoporous materials in the film is 3.0nm or 6.0nm. Compared with a hydrothermal synthesis method and a pulping filtration method, the microwave synthesis method has the advantages of higher synthetic rate, less time consumption, lower energy consumption, higher efficiency and complete structure of formed film materials. In addition, because of the orderliness of the mesoporous structure and the nanometer size effect of the pore diameter, the organic-inorganic compound mesoporous film can be applied inthe fields of embedment of biological molecules, biological sensors and the like.