Abstract: In this study, a turbine bypass valve was used to adjusting the energy distribution ratio of two-stage turbocharger system and fuel air equivalence ratio, and the contradiction between emissions and thermal efficiency was coordinated in a WP12 heavy duty diesel engine. The research showed that with the increase of the turbine bypass valve, the expansion ratio and pressure ratio of the high pressure stage turbocharger were reduced. Then the intake air flow rate was also reduced. The reducing intake air resulting in soot emissions deterioration and useful work was significantly reduced. However, it had slight changes with air exchange work. All these causes the decline in thermal efficiency when diesel working in low-speed conditions. It also showed that adjusting turbine bypass valve to 8% in middle or high speed conditions could increase effective thermal efficiency, and keep emission without deterioration.