In this study, a three-dimensional numerical model of a hydrogen direct injection engine was built, and the effects of several engine operating parameters, including equivalence ratio, injection timing, ignition timing and intake pressure on combustion were analyzed. The results show that with a fixed ignition timing and intake pressure of 1.0 bar, an increase in the equivalence ratio from 0.3 to 1.1 leads to a reduction in indicated thermal efficiency from 47.3% to 37.73% due to increasing wall heat loss. The NOX emissions first increase and then decrease, arriving the peak at the equivalence ratio of 0.7, about 20.9g/kW·h, primarily attributed to the combined effect of oxygen content, cylinder temperature, and hydrogen reducibility. When the equivalence ratio is fixed at 0.5, with the injection timing delayed, the stratification of the mixture becomes more obvious, the combustion speed accelerates, and the maximum thermal efficiency increases. At the same time, NOX emissions also increase due to local high temperature in the cylinder. Furthermore, at the same equivalence ratio, increasing intake pressure reduces the proportion of wall heat loss, resulting in increased maximum thermal efficiency. Nevertheless, the rise in hydrogen mass increases the MMF2500K within the cylinder, leading to an increase in NOX emissions.