In this study the optimal control of fed-batch glycerol fermentation is investigated based on an impulsive dynamical system. Considering the sudden increase of the glycerol and alkali in fed-batch culture of biodissimilation of glycerol to 1,3-propanediol, this paper proposes a non-linear impulsive system of fed-batch culture. The existence, uniqueness and regularity properties of piecewise solution for the system are proved. In view of the controllability of volumes of glycerol added to the reactor instantaneously, the paper constructs an optimal control model based on the nonlinear impulsive system and the existence of the optimal control is obtained. The control variables here are the moments and the sizes of jumps in the states at the discrete instants and the objective is to maximize the productivity of 1,3-propanediol over one cycle.