In order to propose the control strategies based on exergy to realize efficient and energy-saving operation of the engine, the energy and exergy balance under sensitive boundary conditions were analyzed with the first and second laws of thermodynamics on a six-cylinders, four strokes, turbocharged, intercooled, and high-pressure common rail diesel/natural gas (NG) dual-fuel engine in this paper. The results depicted that the thermal efficiency and exergy efficiency decrease with the increase of NG percentage energy substitution rate (PES). Compared with other conditions, at medium load, 1978 rpm and 90% PES, the exergy destruction caused by irreversibility process including mixing combustion, heat transfer and mechanical friction reaches 72.33%. With the advance of diesel injection time (Tinj), thermal efficiency and energy fraction of heat transfer increase first and then decrease. However, diesel injection pressure (Pinj) has little effect on improving energy utilization. Compared with single diesel injection, appropriate multiple diesel injection can improve combustion performance and energy utilization. When the first Tinj is 35 deg CA BTDC and second Tinj is 25 deg CA BTDC, nearly 50% of the energy lost in heat transfer can be converted into useful work. The lost exergy can be reduced by choosing appreciate Tinj and Pinj, adding exhaust gas recirculation (EGR) to reduce in-cylinder temperature to improve combustion and using thermal insulation materials to reduce heat transfer or using the lost heat in other processes such as preheating intake air and producing the hot water or steam of external consumption to reduce the exergy destruction.