The invention relates to a high-flux virus-removing polyvinylidene fluoride hollow fiber microporous membrane with a multi-layer filtering structure and a preparation method thereof. In order to improve the virus interception performance and the pure water flux of the hollow fiber microporous membrane, the polyvinylidene fluoride hollow fiber microporous membrane disclosed by the invention has theadvantages that the outer diameter of membrane filaments is 1.1-1.4 mm, the inner diameter is 0.6-0.8 mm, and the wall thickness is 0.2-0.4 mm, obvious holes are formed in the outer surfaces of the membrane filaments, and a three-layer film pore structure layer with a remarkable boundary is formed from outside to inside. The preparation method comprises the following steps: preparing a membrane casting solution, extruding a hollow fiber membrane, spraying a solvent on the outer layer and exchanging to form a film, performing low-temperature split-phase film forming on the middle layer, carrying out inner-layer low-temperature split-phase film formation and carrying out extraction. The method is based on a thermally induced phase separation membrane preparation method, technologies such asshallow solvent-non-solvent rapid exchange film formation and graded temperature gradient split-phase pore formation are combined, the hollow fiber membrane with the three-layer pore structure, whichhas obvious different boundaries, is prepared by using the method disclosed by the invention, on the premise of ensuring large filtration flux, efficient multi-layer filtration can be formed on pathogenic microorganisms such as viruses, the interception performance reaches 99.99%, and the average interception rate detected by a third party reaches 99.999%.