A three-dimensional simulation on flow behavior and lean combustion in a hydrogen direct-injection gasoline rotary engine was implemented. The combined influence of hydrogen injection pressure (HIP) and nozzle diameter (HND) was numerically analyzed in the critical injection state. Results showed that with the increments of HIP and HND, further penetration and larger dispersion angle of jet-flow were presented. Increasing HIP led to larger jet-flow area and more jet-wall interaction, as well as greater deflection degree of hydrogen-flow after crashing upon the rotor surface. High-speed region expanded, while more jet-wall impingement occurred with the increment of HND. The spark ignited earlier and flame propagated faster as the HND modified smaller. As the HIP increased, the flame speed decreased slightly. The difference in the local Phi distribution and in-cylinder velocity field were the intrinsic mechanism of the HND impact, and the variation in the mixture concentration and TKE magnitude were the root causes of the HIP effect. The pressure and HRR traces were shifted to the downward clearly, while the peak positions were forming later as the HND extended larger. No perceptible difference in the peak positions of pressure and HRR were obtained with the HIP decrease, although pressure tended to increase along with heat release retard to be shortened. The combustion rate decreased with increments of HND and HIP, the timings of the initial consumption were delayed, and a proportional correspondence of reactants and intermediates was witnessed. The reduced NOx formation was obtained by increments of HND and HIP, and an inverse correlation can be seen between soot, CO, HC generations and NOx concentration. The scheme of 0.4 Willa HIP and 1 nun HND was the optimum configuration. Compared with a larger HND and higher HIP configuration, the peak pressure and maximum HRR were increased by 24.1% and 40.5%, and the productions of soot, CO, and HC were reduced by 55.7%, 61.5%, and 54.7%, respectively, though the NOx generation was increased to some extent. It was recommended in practice operations that the combination of lower HIP and smaller HND left a positive influence on improving the combustion characteristics of Wankel engines.