The essence of subgrade mud pumping under train load is the migration of fine particles in subgrade soil. The migration of fine particles will change the pore structure of overlying gravel, thus affect the mechanical and hydraulic properties of gravel layer. To study the influence of fine particle migration from subgrade soil on the microscopic pore structure of gravel layer under cyclic loading, a series of tests are carried out by a self-developed subgrade mud pumping test model, combined with X-ray computed tomography (CT) scanning technology. It has been shown that under cyclic loading, compression of the gravel pores and clogging of migrated fine particles not only change the distribution characteristics of gravel plane porosity, but also decrease the porosity and porosity connectivity. Moreover, the characteristics of the pore size distribution are not affected by loading. The pores of the gravel layer show features of more small pores and fewer large pores, and the characteristic curves of the pore distribution satisfy log-normal distribution before and after loading. However, with the application of cyclic load, the total number of pores decreases. The distribution of pore shape parameters (slenderness ratio and flatness) shows a normal distribution characteristic. The slenderness ratio has not changed significantly with the number of cycles, while the distribution of flatness is more uniform after loading. The pores of the gravel layer have a distinct fractal character. In addition, the three-dimensional fractal dimension of the pores is distributed between 2.40 and 2.50 before loading. With the application of cyclic loading, the three-dimensional fractal dimension gradually decreases.