In order to investigate the deformation characteristic and transport behavior of oil-water micro-interface and its evolution law under different wettability conditions in water flooding, a Hele-Shaw cylindrical model has been constructed based on the N-S equation. Phase field method has been employed to track the topological deformation characteristics of oil-water micro-interface in water flooding. The effect of wettability, oil-water viscosity ratio, and capillary number on the deformation characteristic and evolution process of oil-water micro-interfaces has been studied. The simulation results show that the dynamic evolution process of oil-water micro-interfaces observed from the model surface in water flooding can be divided into four stages, including breakthrough, fracture, three-phase contact line intersection, and micro-interface merging. The breakthrough and fracture phenomenon of oil-water micro-interfaces can be observed repeatedly in the displacement process, and is not affected by wettability and rock particle distribution. Three-phase contact line intersection and micro-interface merging phenomenon have the similar deformation characteristics and evolution law in the vertical profile of the model, which are mainly influenced by wettability and rock particle distribution. Three-phase contact line intersection phenomenon occurs more frequently under water-wet condition, while the micro-interface merging phenomenon occurs more frequently under oil-wet condition. The change amplitude of displacement front decreases and then increases in water flooding as wettability changes from strong water-wet to strong oilwet, which exhibits the piston-like displacement under weak water-wet condition. The simulation results show that the highest oil displacement efficiency is observed under weak water-wet condition, while the lowest oil displacement efficiency (61.06%) is observed under strong oil-wet condition. Moreover, as the oil-water viscosity ratio increases from 20 to 100, the occurrence rate of three-phase contact line intersection phenomenon decreases, the micro oil displacement efficiency decreases by 8.56%, and the initial displacement pressure also increases under weak water-wet and the same injected pore volume multiple condition. As the capillary number increases from 0.66×10-3 to 2.0×10-3, the occurrence rate of three-phase contact line intersection phenomenon increases, the volumes of residual oil decreases, the micro oil displacement efficiency increases by 9.36%, and the displacement pressure also decreases under weak water-wet and the same injected pore volume multiple condition. This reveals that the micro oil displacement efficiency can be significantly improved by increasing the occurrence rate of three-phase contact line intersection phenomenon under water-wet condition. The research results can enrich the micro flow mechanism in water flooding, and provide a theoretical basis for further explore and utilize the residual oil.