The invention discloses a system and a method for repeatedly capturing microspheres based on pulsed laser. Left optical fiber is connected to the input side of a left optical coupler, the output sideof the left optical coupler is connected through left fused optical fiber, the left fused optical fiber is fused with a capillary, the capillary is fused with right fused optical fiber, the right fused optical fiber is connected with the output side of a right optical coupler, and the input side of the right optical coupler is connected with right optical fiber. Left continuous laser and right continuous laser are simultaneously oppositely emitted into the capillary to form an optical trap trapping region. The left pulse laser and the right pulse laser act on microspheres, and the power of theright pulse laser is adjusted, so the the left pulse laser and the right pulse laser act on the microspheres at the same time, and the microspheres bounce off the original position and move to the inside of the optical trap capture region, so the stable capture of the microspheres can be realized. According to the method, the microspheres are separated from the surface of a microcavity by the pulse laser and enter the optical trap trapping region, so the the branching and trapping of the microspheres can be realized, the repeated trapping of single particles can be realized, repeated loadingof the particles is not needed, and the system can be applied to environments such as air, vacuum and the like.