For the biodiesel-fuel production by methanolysis, the reaction mixture is composed of a methyl-ester phase and a glycerol phase. One of the reactants, triglyceride, is mainly contained in the ester phase. The other reactant, methanol, is easily dissolved in the glycerol phase. Therefore, the methanol in the system is not effectively used for the reaction due to interface mass transfer resistance. An excess amount of methanol is required to increase the conversion in single-step operation. Since the glycerol phase is removed during the operation, a two-step batch operation can effectively intensify the process. In the present study, the optimal operating conditions to increase the conversion are obtained for the methanolysis of rapeseed oil using a KOH catalyst. The distribution ratio of methanol addition in the first step was about 0.8, which is confirmed by a simple reaction model.