Hydrogen internal combustion engine is considered to be one of the promising ways to achieve zero-carbon emissions in the automotive industry. However, the problem of high NOx emissions from hydrogen engines needs to be addressed. Although homogeneous lean-mixture combustion could reduce engine-out NOx emissions, it is necessary to ensure mixing homogeneity to avoid excessive NOx formation from the rich mixture packets. In this study, large-eddy simulations (LES) of a direct-injection hydrogen engine were carried out to assess the hydrogen-air mixing process in forming homogeneous charges with consideration of cyclic variations. The high-speed hydrogen jet flow was modeled in a constant-volume vessel first to verify the LES model. Engine simulations were then performed to study the effects of the injector location (side vs. central), injection pressure, and injector type (pintle vs. outward opening) on the mixing process, mixture homogeneity, and cyclic variations. The results show that the mixture homogeneity and its cyclic variations are influenced by these parameters, and the centrally located pintle injector with an injection pressure of 10 MPa can produce the best mixture homogeneity and minimal cyclic variations among the cases studied.