Abstract: Based on the discrete element method of particles, by constructing damage factors, a parallel-bonded water-weakening model is proposed, and a particle flow code model considering the heterogeneity of the mechanical parameters of the cement is established. The comparison and analysis of the results of indoor experiments and numerical simulations verify the correctness and applicability of the proposed model. The main conclusions are as follows: (1) The heterogeneity of rock cement has certain influences on the macroscopic mechanical properties of rock. As the homogeneity factor increases, the homogeneity of the rock increases, and the uniaxial compressive strength and elastic modulus also increase, which conforms to the exponential function relationship. (2) With the increase of the bond area coefficient, the total amount and growth rate of the stored total strain energy in the rock gradually decrease. (3) In the dry state of the rock, the inclination angle of micro-cracks is concentrated in 80°~100°. As the bond area coefficient increases, the distribution range of the inclination angle of micro-cracks gradually increases. (4) With the increase of the bond area coefficient, the rock fracture surface is denser and the penetration is enhanced. The research results can provide a certain basis and theoretical guidance for the meso-mechanism study on the large deformation of the surrounding rock caused by the water in deep-buried tunnels and the deformation of the wading slope of the reservoir bank.