This paper presents a new kind of Petri net—controlled hybrid Petri nets. A hierarchy scheduling structure based on mathematical programming and controlled hybrid Petri nets is introduced. At the high level, mathematical programming is used to find the optimal instantaneous firing speed for the lower level and send control instruction to the lower level. At the lower level, controlled hybrid Petri nets are used to model the real manufacturing environment and accept the instruction from the upper level. Finally, the continuous process system of a chemical plant is taken as an example for illustration.