For uniflow scavenged two-stroke marine diesel engines, the main function of scavenging process is to replace the burned gas with fresh charge. The end state of scavenging process is integral to the subsequent compression and combustion, thereby affecting the engine’s fuel economy, power output and emissions. In this paper, a complete working cycle of a large marine diesel engine was simulated by using the 3D-CFD software CONVERGE. The model was validated by mesh sensitivity test and experiment data. Based on this calibrated model, the influences of swirl ratio and exhaust valve closing (EVC) timing on the scavenging process were investigated. The parameters evaluating the performance of scavenging process were introduced. The results show that, by adjusting the swirl orientation angle(SOA) from SOA=10° to SOA=30°, different swirl ratios are generated and have obvious differences in flow characteristics and scavenging performance. Advancing or delaying the EVC has limited effects on scavenging efficiency, but have obvious effects on the retaining and charging efficiency. In addition, adjusting the EVC timings also have obvious effects on the in-cylinder pressure and temperature, thus affecting the engine’s fuel economy and emission.