Abstract: Two-phase displacement flow in rough rock fractures is prevalent in many engineering applications, and aperture distribution characteristics and wettability of rough-walled rock fractures are the two significant factors that affect two-phase displacement flow behavior. Three-dimensional rough surfaces of fracture were generated based on fractal theory and the homogenous model with homogenous aperture distribution and heterogeneous model with heterogeneous aperture distribution were established respectively. Quasi-static drainage process through rough fractures was simulated using LBM pseudo-potential model, accordingly the effect of aperture distribution and wettability of fracture and its microscopic mechanism on two-phase displacement flow behavior were studied. The displacement front of homogenous model basically maintained stable movement, while the phenomenon of dominant displacement path that preferentially invading larger-aperture area with smaller displacement resistance occurred in heterogeneous model. Enhanced wettability can exacerbate this phenomenon, leading to faster breakthrough of the displacement front, which has no significant effect on the homogenous model. Residual capture can be divided into isolated “trapped” pattern and “water-film” mode that adsorbed on the fracture wall, heterogeneous model obviously had more trapped capture than homogenous model, and strong wettability was beneficial for increasing water-film capture. When the displacement pressure increases to the entry pressure, some wetting phases in small-aperture regions of heterogeneous model are gradually displaced, while most of wetting phases in homogenous model are rapidly invaded, thus the P_c-S_w relation curves of heterogeneous model were gentler than that of homogenous model, and increasing wettability resulted in higher entry pressure at the beginning of displacement for both two fracture models and lower displacement efficiency when the same displacement pressure was imposed.