To enhance combustion and emission characteristics in hydrogen-powered CI engines, this study numerically examined the impact of injector hole variation using a single-cylinder model. Transitioning from diesel-only combustion to dual-fuel hydrogen–diesel operation significantly improved performance. The ISFC decreased by 11.9%, from 461.71 g/kWh (D_2H) to 406.71 g/kWh (D + H_3H), while thermal efficiency increased by 4.5%, reaching 23.05% with the three-hole hydrogen injector. These improvements highlight the benefit of hydrogen’s clean-burning properties and efficient combustion behavior when directly injected at TDC. The variation in injector hole number had a measurable effect on emissions. UHC emissions decreased by 32.4%, and soot emissions dropped by 25.1% when using a three-hole injector compared to the baseline diesel case. These reductions are attributed to enhanced atomization, more uniform fuel–air mixing, and the carbon-free nature of hydrogen fuel. Overall, the results demonstrate that optimizing injector design particularly increasing the number of holes can significantly improve combustion efficiency while reducing harmful emissions in hydrogen-assisted CI engine applications.