FD-3 is a new screened strain that can biodegrade dibenzothiophene (DBT), a model compound in biodesulfurization research work, called Agrobacterium radiobacter. It converts DBT to 2-hydrobiphenyl (2–HBP).The organosulfur in diesel can be removed by FD-3. It not reduces the surful’s content in oil, but can’t destroy the carbon skeleton. This study researched the desulfurization characteristics of FD-3 resting cell to diesel oil organosulfur, and choice the best process by orthogonal experiments.