The scavenging process in two-stroke marine engines not only transports burnt gas out of the cylinder but also provides fresh air for the next cycle, thereby significantly affecting the engine performance. In order to enhance fuel-air mixing, the scavenging process usually generates swirling flow in uniflow-type scavenging engines. The scavenging stability directly determines the scavenging efficiency and even influences fuel-air mixing, combustion, and emission of the engine. In the present study, a computational fluid dynamics (CFD) analysis of the scavenging process in a steady-state scavenging flow test is conducted. A precession phenomenon is found in the high swirl model, and Proper Orthogonal Decomposition (POD) method is used to analyze the reason and the multi-scale characteristics of the precession phenomenon.