In order to optimize the 2-stroke uniflow engine performance on vehicle applications, numerical analysis has been introduced, 3D CFD model has been built for the optimization of intake charge organization. The scavenging process was investigated and the intake port design details were improved. Then the output data from 3D CFD calculation were applied to a 1D engine model to process the analysis on engine performance. The boost system optimization of the engine has been carried out also. Furthermore, a vehicle model was also set up to investigate the engine in-vehicle performance.