The two-stroke engine is a common power source for small and medium-sized unmanned aerial vehicles (UAV), which has wide civil and military applications. To improve the engine performance, we chose a prototype two-stroke small areoengine, and optimized the geometric parameters of the scavenging ports by performing one-dimensional (1D) and three-dimensional (3D) computational fluid dynamics (CFD) coupling simulations. The prototype engine is tested on a dynamometer to measure in-cylinder pressure curves, as a reference for subsequent simulations. A GT Power simulation model is established and validated against experimental data to provide initial conditions and boundary conditions for the subsequent AVL FIRE simulations. Four parameters are considered as optimal design factors in this research: Tilt angle of the central scavenging port, tilt angle of lateral scavenging ports, slip angle of lateral scavenging ports, and width ratio of the central scavenging port. An evaluation objective function based on the Benson/Bradham model is selected as the optimization goal. Two different operating conditions, including the take-off and cruise of the UAV are considered. The results include: (1) Orthogonal experiments are analyzed, and the significance of parameters are discussed; (2) the best factors combination is concluded, followed by simulation verification; (3) results before and after optimization are compared in details, including specific scavenging indexes (delivery ratio, trapping efficiency, scavenging efficiency, etc.), conventional performance indicators, and the sectional views of gas composition distribution inside the cylinder.