Based on the phenomenon that the change of flow state caused by the wall roughness, in order to research the effect of micro structure on the surface of the inner wall of the high pressure homogenization cavity in the high pressure homogenizer to homogenization performance, the groove micro structure is structured on the inner of smooth homogenization cavity, and a computer fluid dynamics (CFD) technique is used to model the two-phase flow in a high pressure homogenizer. This paper will study the high pressure homogenization cavity in the APV-high pressure homogenizer, the oil-water emulsion as the homogeneous materials, the smooth homogeneous cavity and the rectangular section groove homogeneous cavity and the triangular section groove homogeneous cavity are simulated and calculated respectively, and the results are compared. The results show that the homogeneous cavity with groove which has a smaller particle size than the smooth homogeneous cavity after homogenization, the rectangular section groove homogeneous cavity has a smaller particle size than the triangular section groove homogeneous cavity after homogenization, at the same time the particle size distribution is more uniform, improved the homogeneous performance. The results of computer simulation to the results trend obtained by the theoretical analysis of the turbulent near-wall region shows very good agreement.