To enhance the bearing capacity of permeable pavers, cement hardening measures are often used below the brick, resulting in a decline in permeability. To solve this problem, permeable pavers with stone infiltration wells were added. The stone infiltration wells have a decreased permeability due to the retention of particulate matter from the external environment. The influence of different types of blockages on the clogging of stone infiltration wells was studied, and the structure of the stone infiltration wells was optimized by changing the grain size of the stone. The results show that the grain size of the stone affects its resistance to clogging. When the grain size is from 20 mm to 30 mm, the stone infiltration well can maintain good permeability under the influence of clogging.