To research the quality of the hydrogen–air mixture formation and the combustion characteristics of the hydrogen fueled engine under different hydrogen injection timings, nozzle hole positions and nozzle hole diameter, a three-dimensional simulation model for a PFI hydrogen internal combustion engine with the inlet, outlet, valves and cylinder was established using AVL Fire software. In the maximum torque condition, research focused on the variation law of the total hydrogen mass in the cylinder and inlet and the space distribution characteristics and variation law of velocity field, concentration field and turbulent kinetic energy under different hydrogen injection parameters (injection timings, nozzle hole positions and nozzle hole area) in order to reveal the influence of these parameters on hydrogen–air mixture formation process. Then the formation quality of hydrogen–air mixture was comprehensively evaluated according to the mixture uniformity coefficient, the remnant hydrogen percentage in the inlet and restraining abnormal combustion (such as preignition and backfire). The results showed that the three hydrogen injection parameters have important influence on the forming quality of hydrogen–air mixture and combustion state. The reasonable choice of the nozzle hole position of hydrogen, nozzle hole diameter and the hydrogen injection time can improve the uniformity of the hydrogen–air mixing in the cylinder of the hydrogen internal combustion engine, and the combustion heat release reaction is more reasonable. At the end of the compression stroke, the equivalence ratio uniform coefficient increased at first and then decreased with the beginning of the hydrogen injection. When hydrogen injection starting point was with 410–430°CA, equivalence ratio uniform coefficient was larger, and ignition delay period was shorter so that the combustion performance index was also good. And remnant hydrogen percentage in the inlet was less, high concentration of mixed gas in the vicinity of the inlet valve also gathered less, thus suppressing the preignition and backfire. With the increase of the distance between the nozzle and the inlet valve, the selection of the hydrogen injection period is narrowed, and the optimum hydrogen injection time was also ahead of time. The results also showed that it was favorable for the formation of uniform mixing gas when the nozzle hole diameter was 4 mm.