Characterizing the trapped phase in porous media is essential for many engineering applications, such as enhanced oil recovery, nuclear storage, and geological sequestration of CO2. This study aims to study the distribution, evolution, and influencing factors of the remaining oil in the process of water flooding at the pore scale. The single-connected pore space model was established by reconstructing the real micron CT scanned images of carbonate rocks. The VOF (volume of fluid) method using FSF (filtered surface force) formulation was adopted on OpenFOAM platform to simulate the oil-water two-phase flow process at the pore scale. Different wettability and capillary number were considered in the model. The accuracy of the model was proved by comparing with previous experimental results. The results showed that in the process of water flooding, the complex pore structure would lead to the generation of remaining oil, and the phase circulation phenomenon can be observed in the remaining oil and presents two distribution forms: co-current driven flow and lid-cavity driven flow. It also revealed that the phase recirculation increases the viscous dissipation. Further research also showed that the two forms of recirculation could be transferred by changing the wettability and that a higher capillary number was more beneficial for reducing the remaining oil saturation.