A significant part of energy of fuel supplied is lost in internal combustion engines in the form of atmospheric discharge of engine exhaust gases which are considered as a big source of engine inefficiency and formation of pollutant emissions. To address this issue, a bottoming cycle combining the transcritical CO2 (T-CO2) refrigeration cycle and the supercritical CO2 (sCO2) power cycle is employed, aiming to produce cooling for food preservation by utilizing the exhaust heat of homogeneous charge compression ignition (HCCI) engine powering the refrigerated truck. The operative variables and their effect on thermal and exergetic efficiency of HCCI engine and the combined system are investigated. At the base case operative conditions, the thermal and exergy efficiencies of natural gas fueled HCCI engine are improved significantly from 48.69% to 61.28% and from 41.14% to 42.79%, respectively, after employing the sCO2 powered T-CO2 refrigeration cycle. Promotion of equivalence ratio from 0.3 to 0.9 enhances the thermal and exergy efficiencies of HCCI engine from 47.44% to 49.54% and from 40.14% to 42.12%, respectively. Increasing of engine speed from 1400 r.p.m to 2200 r.p.m provides marginal improvement in HCCI engine efficiencies but the efficiencies of combined cycle are significantly improved from 57.67% to 65.18% and from 40.64% to 45.06%, respectively. Finally, exergy analysis applied to determine the sources of non-idealities within the system revealed that out 361 kW (100%) fuel exergy supplied to the system, HCCI engine destroys 93.31 kW (25.85%), catalytic convertor destroys15.49 kW (4.29%), and the in-cylinder heat transfer losses and system exhaust losses are found as 35.72 kW (9.91%) and 16.61 kW (4.61%), respectively.