This study investigates a heavy duty diesel engine with swept vol. 12.6L, 4cycle-OHC type to verify the effects of the performance and exhaust gas emission according to the variable specifications of both swirl ratio and flow coefficient in inlet port, combustion bowl and fuel injection system. To meet the high BMEP and stringent exhaust emission standard, a turbocharger with wastegate and an intercooler were installed in the engine. Helical port, major design parameters for combustion chamber and electronic fuel injection pump with 1,000bar were reviewed and applied. Confirmation tests were also performed to meet the target value, $NO_x$ 5.0g/kWh and PM 0.1g/kWh of Euro3 exhaust emission legislation. The results of this study show that not only is it effective to use a relatively bigger bowl size for controlling rapid burning condition due to the decreased in-bowl swirl, but also to use a concave cam with double injection rates to decrease $NO_x$.