Due to the rising price of crude oil, biofuel as an alternative for fossil fuels is sought to be a global solution to reduce the emission of greenhouse gas. Diesel blended with bio fuel is widely adopted in many countries nowadays. The Taiwan government also enforced the adoption of B2 since 2010. However, suspense on the engine durability caused by biofuel never ends, especially on after treatment system. Selective catalytic reduction system (SCR) has been utilized recently to reduce the NOX emission so as to meet the Euro IV and V emission standards. In order to evaluate the impact of biodiesel on the durability of engine equipped with SCR system, a long-term testing program was organized in this study. The results could be used as the reference to the consideration of marketing promotion strategy as well as government policy in Taiwan. B8 diesel fuel (8 vol% biodiesel) was employed to a commercial heavy duty common-rail fuel injection engine for testing purpose to understand the influence on durability of engine components and SCR system. After 1000-hour full load test operation, the key components of the engines, including injector, piston ring, and catalyst were analyzed and characterized by a series of inspections to identify the degree of decay and wear behavior. In addition, the engine performance was evaluated with SAE J1995 test procedure and the emission was measured by the ETC test procedure at each maintenance stage and after the durability test to determine the variation of performance and emission. Furthermore, the non-regulatory emissions, such as PM2.5,PM diameter distributions, and particle numbers which have been proved to be critically important in causing cancer issues from diesel engine emissions were also evaluated in this study. It was found that the standard deviation of performance and emissions varied under 3% when diesel engine was fueled with B8 biodiesel. The results also indicated that the SCR system still maintained conversion efficiency at 70~95% after 1000hr durability tests.