Soil pore size distribution and pore functional characteristics are the most important for soil physical properties, water retention, and transmission. Furthermore, considerable amounts of rock fragments are present in hilly region soils. In this study, we discuss the pore size distribution and pore functional characteristics of soils as affected by rock fragments in the hilly regions of Sichuan Basin, China. The soil water characteristic curve was measured to calculate the soil total porosity and the ratio of equivalent pores in each diameter class. The results suggest that the soil total porosity decreases with increasing rock fragments size. The proportion of transmission pores increased gradually with increasing rock fragment content, whereas the fractions of storage pores and residual-bonding pores decrease gradually. Furthermore, the ratio of effective soil porosity to total porosity is higher than that of ineffective porosity to total porosity with increasing rock fragment content. In summary, increasing the rock fragment content can notably increase the proportion of soil transmission pores, thereby increasing soil aeration and water permeability. However, a high rock fragment content is not conducive to maintaining the water needed for normal plant growth.