To develop a low emission engine, it is necessary to obtain some better quality of automotive fuels. Sulfur in fuel is transformed to sulfate-laden PM as DOC is applied. Therefore, it necessary to provide low sulfur fuels before DOC is applied. According to the specification of test fuels, flash point, distillation 90％, cetane index are improved but viscosity is decreased in the process of desulfurization. Excessively reduced sulfur may cause to decrease lubricity of fuel and engine performance in fuel injection system. Therefore, this research was emphasized how the application of Bio-diesel affects on the emission characteristics and engine performance under the circumstance of ULSD and DOC.