In order to study the effect of flowing water scouring on the mechanical properties of cement grouting materials, uniaxial compression tests were carried out on residual grout stone body after flowing water scouring. The microstructure of stone body was characterized by nuclear magnetic resonance and scanning electron microscopy. The effect mechanism of flowing water scouring on the mechanical properties of cement grouting materials was discussed in combination with microstructure. The results show that the uniaxial compressive strength and elastic modulus of grouting material decrease significantly due to flowing water scouring, and the attenuation degree becomes more significant with the increase of water flow velocity. At the same time, the peak strain and ultimate strain of residual grout stone body are reduced. When the water flow velocity reaches 1.0 m/s, the residual grout stone body shows obvious brittle failure characteristics. In addition, the number of micropores in residual grout stone body increases significantly, which is the main reason for the attenuation of its mechanical properties. This study is helpful to understand the real mechanical properties of grouting materials in flowing water scouring environment.