Direct injection (DI) technology can improve the combustion performance of the rotary engine by realizing the fuel stratification in the cylinder. The purpose of this paper is to numerically investigate the influence of hydrogen DI strategy on the combustion process in a DI natural gas/hydrogen rotary engine. In addition, it should be noted that the apex seal leakage (ASL) problem is difficult to avoid in the actual work process of the rotary engine. Meanwhile, the ASL flow can significantly change the fuel movement and flame propagation in the rotary engine. Therefore, the action of ASL cannot be ignored for the in-depth study of the combustion process. In this paper a 3D dynamic simulation model considering ASL was first established and verified by particle image velocimetry (PIV) results and in-cylinder-pressure experiment results. Further, based on the established 3D model, the fuel movement and flame propagation process of the DI natural gas/hydrogen rotary engine under varied hydrogen injection position and hydrogen injection timing were numerically studied. By comparing the fuel distribution and combustion speed of all calculation cases, an ideal hydrogen distribution which could improve the engine combustion efficiency was obtained. The ideal hydrogen distribution is that, under the premise of ensuring minimized hydrogen leakage, the hydrogen should mainly distribute in the middle and front of the cylinder, and a high hydrogen concentration should distribute around the spark plug. Under the guidance of the research results of this paper, to promote the engine combustion performance in the actual engine development, the position which is located at the intersection between the cylinder form line and the major axis is recommended as the installation position of the hydrogen nozzle, and 240 degrees CA (BTDC) is recommended as the injection timing of the hydrogen nozzle.