Currently the downsizing of IC Engine has become the mainstream to meet fuel economy and emission regulations. It is required that higher power output while with lighter weight that is actually a daunting challenge for a common four-stroke IC engine, because it needs lots of new technologies and high manufacturing cost. For recent years the two-stroke opposed piston engine has drawn much attention in many developed countries for fundamental advantages itself. Double firing frequency means the increased power density brings about smaller engine size and lighter weight. However, the low scavenge efficiency has been assumed the main disadvantage for a two-stroke engine for a long period, and adverse to combustion efficiency. The uniflow scavenging process was investigated by the transient CFD simulation for multiple Cases. The influence of port timing and exhaust back pressure on scavenging was analyzed for two different intake port layouts. The calculated results are shown that exhaust back pressure dominates the charge air leakage and trapped air mass in cylinder. The pressure drop between intake port and exhaust port is whether too high or low all will cause a non-ideal scavenge efficiency affected by final trapped air mass. In addition, the port timing is also quite important to efficiently control the fresh air escape from cylinder, and improves the scavenging process. The intake port orientation based on a datum line will impose a slight effect on scavenge efficiency compared to port timing and exhaust back pressure. In terms of results in all Cases the relative perfect design scheme is Case02 with positive tilt angle for new port timing, and it’s scavenge efficiency is over 90% at 3500rpm with full load and rated power speed in a two-stroke opposed piston engine.