In order to address the problem of the real-time scheduling and control of batch chemical systems, this work proposes a model predictive control method based on Petri nets. First, a method is presented to construct a batch chemical system’s timed Petri net model. Second, a control structure is designed to augment the Petri net model to control the valves. This results in timed Petri nets that formally represent the process specifications of a batch chemical system. Third, a model predictive control method is developed to schedule and control timed Petri nets, where a proposed heuristic function is utilized to perform the optimization computation. The model parameters are dynamically adjusted using online data, and both scheduling and valve control instructions are calculated in real time. Finally, a series of experiments is carried out in a beer canning plant to verify the proposed method. According to the experimental results, the scheduling and control problem can be solved in real time, where the online computations can be performed in milliseconds, and the resulting scheduling strategies are optimal or near-optimal.