The reliability of three-dimensional discrete element numerical simulation of granular materials depends on the reasonable calibration of mesoscopic parameters. At present, systematic research on the calibration method of mesoscopic parameters is lacking. Based on the comparative analysis of indoor direct shear test and numerical simulation, the correlation between the macroscopic mechanical parameters of granular materials and the mesoscopic parameters of particles was revealed. Besides, the calibration method of the meso parameters of the numerical simulation of granular materials was proposed, and the rationality of the calibration method was verified. The research result showed that: in the linear model, the macro elastic constant of the sample was positively correlated with the normal contact stiffness of the particles, but not sensitive to the change of the tangential contact stiffness. Based on this, the calibration method of contact stiffness (normal and tangential) of particles was proposed. The shear stress-shear displacement curve of the numerical direct shear test was well agreed with the experimental value, so the reliability and rationality of the calibration method were verified; Through the numerical test of the direct shear of gravel, it was found that the internal force chain network of the particles deflected from the vertical direction to the diagonal direction of the shear box with the increase of shear displacement, and the shear shrinkage and expansion occurred with the change of the overall velocity field of the particles during the shear process. The meso parameter calibration method proposed was used to conduct a numerical simulation of an indoor landslide motion test. The morphology of landslide gravel accumulation in the numerical simulation was consistent with the indoor test result, which verified the applicability of the calibration method in the simulation analysis of accumulated gravel landslide.