The invention relates to a preparation method of a nuclear pore filter membrane and particularly relates to a nuclear pore filter membrane with a pore passage structure combined by a cone-shaped pore passage and a columnar pore passage. A preparation method of the nuclear pore filter membrane with tthe compound pore passage structure mainly comprises the following steps: radiating a polymer film by virtue of high-energy heavy ions, so as to form a latent trace; respectively etching the same surface of the radiated polymer film by virtue of two etching solutions with different track etching speeds, so as to form the novel cone/column compound pore passage structure. The cone/column compound pore passage structure has the obvious structural characteristics that the pore passage is formed by the linkage of an upper part and a lower part, and specifically comprises the cone-shaped pore passage and the columnar pore passage; the columnar pore passage is etched and machined by virtue of liquid with high track etching speed; the cone-shaped pore passage is etched and machined by virtue of liquid with the lower track etching speed. By utilizing the novel pore passage design, the technical problem of low filtration flux of the small-aperture nuclear pore filter membrane can be beneficially solved, and the technical problems of single-layer filtration and repeated cleaning are further beneficially solved.