The complex in-cylinder gas state and flow significantly affect fuel-air mixture, combustion efficiency and emissions. However, the scavenging CFD model of large bore marine engines in digital twin system requires substantial computational resources. Therefore, a fast-run phenomenological model of the scavenging process is built in this study. The model simulates the thermal states and flow dynamics of inlet and exhaust gas based on the energy and momentum conservation principles, considering the ideal in-cylinder swirl velocity profile with effects of air mass loss, wall friction, and swirl shear. The model’s accuracy is confirmed by comparing it with CFD simulations on different engines, showing an average relative error less than 3.5%. It also analyzes the impacts of intake pressure. The model provides accurate boundary conditions for subsequent fuel spray, combustion, and emission simulations and can be combined with these models in the future, thereby applied to engine design, diagnostics, and control.