To achieve more stringent exhaust emission regulations will face more and more daunting challenges nowadays. It needs more new technologies to improve the IC engine performance but needing higher costs in order to meet Euro 6 and EPA standards in USA. Recently the opposed-piston engine (OPE) has been treated as the promising product to meet these new regulations but relatively lower costing. Although two-stroke OPE owning inherent thermal efficiency and power density advantages, the inefficient scavenge efficiency appears to become the main obstacle to enhance combustion efficiency whilst reducing exhaust gas emission. For the improvement of scavenge efficiency the transient gas exchange simulation was carried out for multiple Cases here, including two intake port configurations at various back pressures in exhaust system and two port timings. The effects of exhausting back pressure, porting timing and intake port layout on scavenging and trapped air mass in cylinder all were investigated by transient CFD simulation including blow-down and scavenging. The calculated results showed that for Case02 that intake port entrance orientation with a right tilt angle referred to baseline, the scavenge efficiency is relatively higher than one with left tilt angle in Case01 for different exhausting back pressures, also for trapped fresh air mass. The turbulence kinetic energy is extremely sensitive to back pressure in exhaust chamber. The investigation was also found that the port timing is also quite important for scavenging process and pump losses, and there will be a little increase of scavenge efficiency by about 2-3% via adjusting port timing for both Cases, and the net trapped masses are approximate to each other but with less fresh air leakage for new port timing. Apparently, the exhaust back pressure will impose much more considerable influence on the entire scavenging performance than the port timing, as using uniflow scavenge mode in a two-stroke opposed piston diesel engine.