In Wankel rotary engine (WRE), high mainstream velocity in combustion chamber blocks flame propagating to the end of combustion chamber, which causes high emissions and low combustion efficiency due to unburned mixtures. To solve this problem, a three-dimensional dynamic simulation model of a hydrogen-gasoline blends fueled WRE is built and validated. The in-cylinder mixture formation and combustion process are investigated under different hydrogen injection timing (HIT) and duration (HID) conditions. The study results show that the concentration of hydrogen distributed between the spark plug region and rear combustion chamber increases with retarded HIT and extended HID. Faster flame speeds are obtained for HIT of 110 °CA BTDC and HID of 40 °CA. At a fixed HID of 20 °CA, compared with HITs of 210 and 160 °CA BTDC, the peak in-cylinder pressures for HIT of 110 °CA BTDC are increased by 14.3% and 6.8%, respectively. At a fixed HIT of 110 °CA BTDC, the peak in-cylinder pressure in HID of 40 °CA is 52.3% and 9.21% higher than HIDs of 20 and 30 °CA. The highest in-cylinder pressure is achieved with the hydrogen injection strategy that HIT of 110 °CA BTDC, HID of 40 °CA. However, as the temperature increases with pressure, nitrogen oxide emissions are also increased with retarded HIT and extended HID obviously. Considering the lowest carbon monoxide is achieved and the unburned zone in the rear region of combustion chamber is eliminated in HIT of 110 °CA BTDC, HID of 40 °CA. The hydrogen direct injection strategy that HIT of 110 °CA BTDC, HID of 40 °CA acquires the best engine performance in this research.