The internal structure of sandy cobbles strata is sensitive to disturbances in the urban underground environment, but the structural evolution process under coupling hydraulic and dynamic loads remains unexplored. This paper presents a detailed investigation into the migration patterns and mechanisms of fine particles in sandy cobbles induced by coupled hydraulic and dynamic loading. A sandy cobble specimen with a typical particle size distribution (PSD) was designed and tested using an apparatus that included a constant inlet water head control system and an eccentric-vibrator-based dynamic loading system. Based on physical modeling tests, a numerical model was constructed to replicate the internal structural evolution under hydraulic and dynamic loading by calibrating the time history of local permeability. The test results indicate that the application of dynamic load can instantly disrupt the stable internal structure of sandy cobbles under static seepage, imparting kinetic energy to fine particles that detach from the skeleton structure and migrate along the seepage direction. Significant fine particle loss occurs near the seepage outlet, but due to energy loss during migration, fine particles far from the seepage outlet are recaptured by the skeleton pore throats and clogged again in the migration path. As the intensity of the dynamic loading increases, the migration path for fine particles becomes longer, and the amount and size of fine particles lost significantly increase. The changes in the internal structure of the soil are reflected in hydraulic parameters as a transient increase in local flow velocity, an increase in local pore water pressure due to clogging, and a decrease in the overall permeability coefficient with the loss of fine particles. The findings of this study will be useful for future geotechnical engineering design and analysis.