Artificial groundwater recharge utilizing stormwater is an effective tool to reduce urban flooding and artificially increase groundwater resources. However, porous media clogging due to the solid polydisperse particles carried in stormwater severely restricts the application of recharge technology. In addition, solid particles play a crucial role in aquifer contamination. If particles are easily transport in groundwater flows, they can act as contaminant carriers to facilitate the movement of contaminants. Conversely, if particles cause porous media clogging, they can form barriers that prevent contaminant migration. While the transport and clogging mechanism of particles has been explored by many macroscopic physical experiments, the intrinsic connection between the deposition behavior of particles in pore scale and the macroscopic presentation of clogging phenomenon remains unclear. In this study, laboratory-scale sand column experiments were combined with scanning electron microscopy (SEM) observations to explore the effect of polydisperse particle size on the mechanism of particle transport and clogging. The median particle sizes (d_p50) of the polydisperse particles used in the experiments were 0.66, 4.05, and 11.83 μm, respectively. The interaction energy between particles and porous media grains was calculated using XDLVO theory, indicating that the experiments were conducted under unfavorable condition. The sand column experiments revealed that the influence of large particles on the porous media permeability is limited to shallow layers, and small particles are more likely to transport to deeper layers. Particles with d_p50=0.66 μm were tend to form aggregates, reducing particle recovery rate and promoting clogging. The pore-scale observations illustrated that the vast majority of the particles are preferentially deposited in concave regions of the media grain surface. The larger the particle size, the higher the proportion of deposition in concave regions. Due to the different transport mechanisms of particles in pore space, the ratio of d_p50 to porous media grain size is not the only basis for identifying the type of clogging. The results proved that the particles with d_p50=0.66 μm can form mixed clogging faster than particles with d_p50=4.05 μm. The proposed results provide a reference for the theoretical study of the particle transport and deposition mechanism, the prevention and control of aquifer pollution, as well as the development of more effective artificial groundwater recharge scheme.