Formal methods are proposed to arrange and establish strictness in stages for the development of software. This method assists to avoid serious issues, offer standard resources to record various hypotheses and conclusion and outline a source for stability among many connected activities. Workflow management system assists the administration to define and coordinate different departments such as several employees and systems. By using the workflow management system the administration can control, monitor, optimize the problem and maintain the business process. Formal approaches are used for designing and verification of the proposed system. The organization can save the time of development and implementation of the model. By using Petri net formalism we can design and model the specification and verification of multifaceted workflows. This research work focuses on the methods for modeling, analysis and simulation of workflow management system. A proposed model is developed, which almost eliminate the risks of logical errors before starting the code of the software. In this research work, the workflow model is designed for a railway reservation system. This organization has different reservation offices at different locations. These offices are interlinked with each other. To design a model of this company multi-agent based technique is used and each office works as an agent of the system. This research is intended to design an interaction model for the cooperation between these offices (modules). Petri net formalism is applied for modeling, analysis and verification purposes to show the workflow in between these offices (modules for entire system). This research is intended to design an interaction model for the cooperation between these offices (Agents). By using CPN tool four stations? models are designed and verified their liveness, boundedness and reversibility through invariants. After this these micro models also known as Agents are joined to a single macro model known as Railway Reservation System (RRS), where each Agent represents as a place by using the idea of nets within nets. These agents interact with each other through transitions in macro model. Due to state space explosion it is not possible to analyze each micro model through reachability graph, so analysis is done through place and transition invariants. Macro model is then verified through reachability graph as well as through invariants by using CPN tool and MATLAB.