Traditionally, the task of conjecturing the operation steps in batch processes is carried out manually on an ad hoc basis. This approach is often time-consuming in industrial applications, and furthermore, the resulting recipes may be error-prone. The aim of this paper is thus to develop a systematic strategy to generate the optimal operation procedures with the Petri-net based binary integer programs (BIPs). Specifically, the system net consists of three types of standard subnets, i.e., the path modules, the equipment modules, and the process modules. The logic constraints in the corresponding BIP are formulated mainly for the purpose of describing the token movements in the system net. Additional constraints are also incorporated to enhance solution efficiency. The specific actions in the optimal operating procedure can be determined by solving this integer program. Two distinct classes of operation modes can be identified: (1) stage-based operating procedures and (2) time-based operating procedures. Several realistic examples are provided in this paper to demonstrate the feasibility of the proposed strategy.