The biodiesel attracts attention as a fossil alternative fuel. It has turned out to be effective to use the methoxide type anion-exchange resin as a catalyst for the biodiesel production. However, the problem of the resin deactivation in the fixed bed reactor still remains. The deactivation mechanism of the resin in the reactor for the biodiesel production was investigated. As a result, it was clarified that the contact of the resin with triglycerides of the reactant was obstructed by glycerin of the byproduct absorbed by the resin. It was suggested that increasing the linear velocity in the reactor decreased the adsorption of glycerins, so that the deactivation of the resin could be controlled. Moreover, the setting up drift plates in the reactor could improve the yield of biodiesel.