Hydrogen engines show great potential as a power source with good combustion performance, zero carbon emissions, and diverse sources. However, the exhaust emission characteristics with high water vapor (H2O) content have not yet been clarified. This study presents the exhaust emissions of a heavy-duty direct-injection hydrogen engine under various operational parameters, with a focus on the H2O content. The results reveal important exhaust emissions characteristics of the hydrogen engine, including lower exhaust temperature (200 °C–400 °C), higher unburned H2 emissions (up to 17100 ppm), less nitrogen oxide (NO) generation (<1000 ppm), and higher H2O content (6%–40%). Additionally, unburned H2 rises, and NO and H2O decrease as the excess air ratio (λ) increases. When λ is greater than 3, NO levels fall sharply to below 100 ppm. Optimal emissions performance is achieved with a 5 °CA BTDC ignition timing where low levels of H2, H2O, and NO are maintained. Increasing hydrogen injection pressure decreases H2 but raises exhaust temperature, H2O, and NO emissions. Excessively delaying hydrogen injection timing adversely affects the concentration gradient in the cylinder, increasing unburned H2 emissions. The best emissions performance is observed at a hydrogen injection timing of 110 °CA BTDC.