As a type of alternative fuel, biodiesel has advantages in reducing greenhouse gases and ensuring energy security. Compared with petroleum diesel, biodiesel has different lower calorific value, oxygen content and octane number that would raise problems when the unoptimized common rail diesel engine is fueled with biodiesel or its petroleum diesel blends. Among these problems, decreasing full load torque output and increasing NOx and BSFC are significantly important.Fuel injection parameter calibration and optimization experiments are carried out in an in-line 6-cylinder 8.82 liter turbocharged and intercooled common rail diesel, which is equipped with Denso ECD-U2 fuel injection system, SCR (Selective catalytic reduction) and DPF (diesel particulate filter). To avoid after-treatment apparatus' coupling influence and re-calibration, emission measure point is set in front of catalysts. The experiment adopts B20 biodiesel as test fuel.Firstly, this study re-calibrates the full load fuel injection quantity, makes full load torque output recovered to original status (unadjusted engine fueled with petroleum diesel) when a diesel engine is fueled with B20.Secondly, this study re-calibrates and optimizes the combinations of the fuel injection timing and the common rail pressure, following optimization rules which include minimized NOx and PM emissions and BSFC. Meanwhile, equivalent BSFC and NOx are less than or equal to original status when a diesel engine is fueled with B20.