<p>Against the backdrop of carbon neutrality goals, the application of hydrogen energy in internal combustion engines has increasingly attracted research interest. To clarify the influence of mixture distribution on the combustion characteristics and emissions of hydrogen engines, this study experimentally investigates three mixture formation modes—homogeneous, semi-homogeneous, and stratified—under lean-burn conditions. The results show that, as the start of hydrogen injection (SOI) is delayed, the mixture gradually transitions from a homogeneous to a semi-homogeneous state. Consequently, heat transfer losses decrease, thermal efficiency improves, and the coefficient of variation is reduced. Both the combustion duration and ignition delay shorten, while the combustion rate increases slightly, accompanied by a modest rise in NOx emissions. Further delaying SOI causes the mixture to shift from semi-homogeneous to stratified, resulting in a longer combustion duration, especially during the late combustion phase. Under lean-burn conditions, homogeneous combustion exhibits a relatively low combustion rate, cylinder pressure, and pressure rise rate. In contrast, semi-homogeneous and stratified mixtures show significantly higher combustion rates. Regarding combustion stability, the semi-homogeneous mode exhibits the best stability performance, while both homogeneous and stratified modes show higher cycle-to-cycle variations.</p>