The aim of this research is to investigate the influences of apex seal leakage on the formation mechanism of flow field in a side-ported rotary engine by particle image velocimetry (PIV) and computational fluid dynamics (CFD). In this study, a PIV was used to acquire the two-dimensional (2D) flow field on the rotor housing central plane at an engine speed of 700 rpm. A three-dimensional (3D) dynamic simulation model considering leakage through apex seals was established and verified by the 2D-PIV experiment results. Thereafter, CFD analysis was used to further understand the 3D flow field in combustion chamber under the action of apex seal leakage. The simulation results showed that for the three engine speeds (2000, 3500, and 5000 rpm), in the intake stroke, the vortex generated in the front end of combustion chamber under the condition with no leakage, was strengthened and destroyed by the effects of the small (0.02 mm) and the large (0.08 mm) apex seal leakage gaps, respectively. As the apex seal leakage gap increased, the volume efficiency and the peak pressure decreased continuously. The volume efficiency and the peak pressure caused by any fixed apex seal leakage gap decreased with the increase of the engine speed. Compared with the volumetric efficiency of the condition with no leakage at 2000 and 5000 rpm, the volumetric efficiency of apex seal leakage gap of 0.08 mm decreased only by 24.6% at 5000 rpm, but by 41.2% at 2000 rpm.