Three dimensional discrete element numerical model was established by PFC3D with different boundary conditions, the grinding process was simulated, and the average contact force between balls was also analyzed. The effects of different milling factors on the superfine pulverization of notoginseng were investigated, and the simulation results were proved through the single factor experiments. The results showed that the order of key factors, which affected the milling process was rotation speed, ball material ratio and mass ratio of balls. The optimum conditions were as followed: the rotation speed of 500 r/min, ball material ratio of 8 to 1, and mass ratio of balls of 1 to 4, which provide the reference for the design of orthogonal experiments.