The microsphere system has small initial particle size, excellent swelling performance, simple manufacturing process, and strong plugging ability. It has great application potential in the field of plugging and profile control of deep reservoirs. Microspheres can effectively plug the pores of fractured cores, inhibit the rapid breakthrough process, and improve the sweep efficiency of the injected fluids. However, the microscopic plugging mechanism of microspheres on fractured cores is still unclear. In this study, the distribution of microspheres after plugging was observed through specially prepared core models. Furthermore, the microscopic plugging mechanism of microspheres in fractured reservoir cores was clarified, including direct microsphere plugging, cluster bridging plugging, adhesion plugging, extrusion-deformation plugging, and extrusion-crushing plugging. Then, particle flow simulation software was used to establish the fluid-solid coupling model of microsphere plugging, and then, the numerical simulation of the plugging process was realized by Python module programming. Through this study, the plugging effect of microspheres under different fracture opening conditions was clarified. Moreover, the effects of injection pressure difference, fracture width, and particle size ratio on the fluid-solid structures of microsphere plugging were analyzed. The results show that the smaller the particle size ratio, the greater the injection pressure difference, the fracture width, and the reduction magnitudes in fracture porosity and core permeability and the higher the plugging rate. The numerical simulation results well support the microsphere plugging mechanism obtained by experiments. The results of this study can provide theoretical and technical support for the development of deep profile control and flooding and enhanced oil recovery technology of the polymer microsphere dispersion system in fractured low-permeability reservoirs.