The Linear Internal Combustion Engine-Linear Generator Integrated System (LICELGIS) is different from conventional crank-based engine for reducing frictional losses by eliminating the crankshaft. Thus, the LICELGIS piston stroke is not constrained geometrically and the system compression ratio is variable. During steady-state operation, the LICELGIS converts the fuel chemical energy into electric power with piston assembly reciprocating motion, which can for example be used as a range-extender in hybrid electric vehicles. The LICELGIS scavenging process is prerequisite and key for the system steady-state operation, which has remarkable influence on mixture gas and, eventually, on engine combustion performance. In order to achieve high scavenging performance, a LICELGIS is investigated in this paper. The LICELGIS motion characteristics and scavenging process were analyzed. A numerical simulation architecture was concentrated on for the investigation of scavenging process by coupling of zero-dimensional (0D) dynamics and three-dimensional (3D) computational fluid dynamics (CFD). The numerical simulation architecture were set up and validated with a LICELGIS prototype tested data. Based on port height and port angle, influence rules of scavenging system structure on scavenging performance were obtained, qualitatively. The simulation results indicate that both port height and angle show significant influence on scavenging process. For improving scavenging efficiency, large height of scavenging and exhaust ports, tangential inclination of chief scavenging port at 65°and axial inclination of sub scavenging port at 50°should be taken into account. For enhancing turbulent kinetic energy of in-cylinder gas, which is in favor of combustion rate, small height of scavenging and exhaust ports, small tangential inclination of main scavenging port and large axial inclination of sub scavenging port should be taken into account.