Particle clogging in the artificial groundwater recharge process is one of the main factors influencing the artificial groundwater recharge efficiency, and particle deposition is the microscopic mechanism of the occurrence and development of particle clogging. Particle deposition in porous media changes the pore structure. The computed tomography (CT) scanning technique is a nondestructive testing method and determines the spatial distribution of pores in porous media. This study combines physical and CT scanning experiments to identify the change process of the pore structure in the artificial groundwater recharge process and compares the pore changes during recharge experiments between two columns containing different media. Porous media changes are observed with the CT scanning technique. The fractal theory is applied in the analysis of CT scan images and physical experiment results. The results of this study indicate that particle deposition can be examined by using CT scan images to obtain pore-related parameters, the internal pore structure of porous media determined through CT scan images can be applied in numerical simulation, and a mathematical model for particle deposition calculation in porous media is established. Compared to the physical experiment measurements, the spatial particle deposition information acquired with the CT scanning technique exhibits a higher accuracy and contains much more relevant data. Not only does this research reveal more clearly the particle clogging mechanism which is based on particle deposition, but also characterize, simulate and predict more accurately the development tendency of particle clogging during artificial groundwater recharge.