Considering the hybrid nature in fed‐batch culture of glycerol biconversion to 1,3‐propanediol (1,3‐PD) by Klebsiella pneumoniae, we propose a state‐based switching dynamical system to describe the fermentation process. To maximize the concentration of 1,3‐PD at the terminal time, an optimal switching control model subject to our proposed switching system and constraints of continuous state inequality and control function is presented. Because the number of the switchings is not known a priori, we reformulate the above optimal control problem as a two‐level optimization problem. An optimization algorithm is developed to seek the optimal solution on the basis of a heuristic approach and control parametrization technique. Numerical results show that, by employing the obtained optimal control strategy, 1,3‐PD concentration at the terminal time can be increased considerably.