Modern-day diesel engines are adapted with new technologies to meet strict emission standards. This study addresses the use of a novel vortex tube air intake system with air from its cold and hot ends to a compression-ignition engine with hydrogen gas addition. Hydrogen energy share is limited to 29% due to the maximum detonation limit. Hydrogen flow rate, diesel injection timing, and injection pressure are maintained to arrive at the maximum brake power and minimal levels of pollutants such as smoke, nitrogen oxides, and particulate matter. For further reduction of engine nitrogen oxide emissions, exhaust gas recirculation and water injection methods are adopted in this study and compared. Energy balance analyses among the supercharged mode with vortex tube and naturally aspirated modes are presented. It is noticed that pollutant levels could be decreased with hydrogen addition with 40% cold air or 60% hot air from the vortex tube intake system. The overall efficiency increases from 28.3% in a naturally aspirated air to 30.1% in the vortex tube intake system with hot air, leading to a 32% comparative increase in brake thermal efficiency. Smoke decreases in the vortex tube intake system by 37%. Soot-NOx and HC-CO tradeoff analyses are also presented.