Significant efforts are currently underway to transform the transportation industry from a fossil fuel-based industry to a hydrogen-based industry to achieve the goal of zero carbon emissions. In this study, hydrogen direct injection (DI) is implemented using three mixture formation modes: homogeneous charge, lean-homogeneous charge, and lean-stratified charge (LSC). The main objective is understanding the effect of the hydrogen mixture mode on the efficiency and emission characteristics of the hydrogen DI engine. Accordingly, hydrogen was used as the fuel in a spray-guided single-cylinder research engine. The results revealed that owing to the high heat loss characteristics of hydrogen, the optimized combustion phasing angle was retarded. The LSC mode minimized heat transfer loss by reducing the high-temperature area near the cold cylinder wall. Furthermore, it had the highest indicated thermal efficiency (ITE) of 34.09 %, especially under low load conditions. However, the stratified rich hydrogen in the LSC mode resulted in high nitrogen oxide emissions (6.68 g/kWh). Heat management is vital to efficiently extract energy from hydrogen in an internal combustion engine. Heat loss reduction (13 %) contributes more to high ITE than pumping loss improvement (2 %) in the LSC mode.