Apex seal leakage is one of the main defects restricting the performance improvement of rotary engines. The aim of this study is to study the airflow movement in a peripheral ported rotary engine under the action of apex seal leakage. For this purpose, a three-dimensional (3D) dynamic calculation model considering apex seal leakage was first established and verified by particle image velocimetry data. Furthermore, based on the established 3D model, the flow field in the combustion chamber under the four apex seal leakage gaps (0.02, 0.04, 0.06, and 0.08 mms) and the three engine revolution speeds (2000, 3500, and 5000 RPMs) was calculated. By comparing with the flow field under the condition without leakage, the influences of the existence of apex seal leakage on the velocity field, the turbulent kinetic energy, and the volumetric efficiency in the combustion chamber were investigated. Thereinto, the influences of the existence of apex seal leakage on the velocity field is that at the intake stroke, a vortex formed in the middle of the combustion chamber under the condition without apex seal leakage, was intensified by the apex seal leakage action. At the compression stroke, irrespective of the condition with or without apex seal leakage, all vortexes in the combustion chamber are gradually broken into a unidirectional flow. However, there is an obvious “leakage flow area” at the end of combustion chamber due to the existence of apex seal leakage.