The invention relates to a multi-layer composite micropore filter separation material, a method for preparing the material and the application thereof, wherein, the preparation method comprises the following steps: (1) the fiber which can be fibrillated is prepared into fully fibrillated fiber material by pulping process; (2) the slurry is obtained after the fully fibrillated fiber material is dispersed in water; (3) advancing to the net and shaping are carried out, a layer of nonwoven fabric is placed on a shaping net, the above slurry is dehydrated on the nonwoven fabric directly for compound molding; (4) drying is carried out for obtaining the product. The product can also be processed by hot press molding. The method can be operated easily, is applicable for application of large scale, the obtained multi-layer composite high temperature resistance micropore filter separation material has the outstanding performance of high temperature resistance, meanwhile the uniformity of the holes is excellent, the average aperture can reach 10nm-1mum, and the method can be used in such fields as preparing filter material, battery septum material, electrolytic capacitor paper and double electric layers capacitor septum, etc.