PurposeThis paper aims to provide a design of intelligent model‐based topology analyzer that can be used to improve plant operation.Design/methodology/approachPOOM process modeling methodology is proposed to model and partition plant topology so that plant operation can be designed in effective manner as mapped to plant topology partitions. Plant topology is divided into areas based on the operation required and material flow and isolation paths are identified automatically using intelligent algorithm.FindingsIt is possible to define hierarchical plant structure (topology) partitions that can be mapped to plant operation levels, which are described by ANSI/ISA‐S88. In addition, the use of design knowledge can be useful to define conceptual partitions such as Block, which is essential to link design and operation knowledge. Plant operation (jobs) can be flexibly defined in view of plant structure partitions in terms of resources (materials, plant structural areas) required and operation scheduling.Research limitations/implicationsIt is important to link to production scheduling to ensure effective use of topology partitions in real time based on available resources. The proposed approach can be improved via the integration with intelligent production scheduling.Practical implicationsProduction and manufacturing plants will be able to use the proposed approach to design and validate plant operation and to improve plant maintenance while reducing operation risks by identifying plant structures required for each operation task. The proposed technique can be helpful to engineers and R&D members to consider in their design and investigation for process safety, risk management, and plant operation and management.Originality/valueThe idea of topology analysis is quite new where it is usually implemented using search algorithms without considering domain knowledge and operation structures. This paper proposes a valuable technique to link plant structure with plant operation hierarchies, which is important for design and engineering practices and R&D activities for plant operation.