As a common solid waste in geotechnical engineering, rock granular material should be properly treated and recycled. Rock granular material often coexists with water when it is used as the filling material in geotechnical engineering. Water flowing in rock granular materials is a complex progress with the mechanical-hydrological-chemical (MHC) coupling effect, i. e. the water scours in the gaps and spaces in the rock granular material structure, produces chemical reactions with rock grains, rock grains squeeze each other under the water pressure and compression leading re-breakage and producing secondary rock grains, the fine rock grains are migrated with water and rushed out. In this process, rock grain size distribution (GSD) changes, it affects the physical and mechanical characteristics of the rock granular materials, and even influences the seepage stability of the rock granular materials. To study the variation of GSD in the rock granular material considering the MHC coupling effect after the seepage process, seepage experiments of rock grain samples are carried out and analyzed in this paper. The result is expected to have a positive impact on further studies of the properties of the rock granular material.