Abstract: The drilling process of lunar soils with a large granular rock under the surface is simulated dynamically by 3D discrete element method. A novel 3D discrete element model considering bending and twist moments and equivalent attractive force is established firstly, and then, a triaxial simulation test is conducted to calibrate the micro-parameters. The mechanical macro-parameters of the model are calculated as follows: the cohesion is 0.90 kPa and the internal friction angle is 42.25°, meeting with those of the real lunar soils. Four working conditions are designed and simulated respectively focusing on the case that a large granular rock exists in the lunar soils. By monitoring the sampling efficiency and the motion trajectory of the rock, the "screwing-in phenomenon", "vertical migration phenomenon" and "blocking phenomenon" are discovered. The results show that the diameter of the "large particle" influences the sampling results directly: when the particle size is smaller than the diameter of the "virtual cutting round" of the drill bit, there are no obvious effects either on the sampling efficiency or on the later winding collection; and the blocking phenomenon will appear, reducing the sampling efficiency badly and probably making the sampling task a failure. The achievements of this work have vital engineering reference value to the design of sampling controller and drill structure.