Internal combustion engines waste a significant amount of energy from the fuel they consume, mostly through the atmospheric release of engine exhaust gases. This phenomenon is well acknowledged as a significant contributor to engine inefficiencies and the production of harmful pollutant emissions. In order to tackle this issue, a bottoming cycle that combines a supercritical CO2 (S–CO2) power cycle with an ejector refrigeration cycle (ERC) is implemented. The goal is to generate power, heating, and cooling utilizing waste heat from a natural gas-powered homogeneous charge compression ignition (HCCI) engine. The study found that the HCCI engine, when not utilizing a bottoming cycle, demonstrated thermal and exergy efficiencies of 48.30% and 40.83%, respectively. However, the incorporation of S–CO2 and ERC cycles resulted in significantly higher system efficiencies of 64.90% and 48.84%, respectively. Furthermore, the proposed system has thermal efficiencies of 53.86% for electrical output, 7.801% for heating output, and 3.239% for cooling output. In addition, the HCCI engine accounts for the most exergy destruction in the system, accounting for 92.83 kW (25.72%), with losses due to in-cylinder heat transfer and system exhaust accounting for 20.63 kW (5.72%) and 12.52 kW (3.47%), respectively.