This paper presents a method for modeling and simulation of particular class of manufacturing systems. The method is based on so called Machine-Job Incidence Matrix (MJI) that is formed from Steward sequencing matrix and Kusiak machine-part incidence matrix. A model of the system in a form of MJI matrix is easy to comprehend. It can be put in direct relation with other manufacturing systems analysis tools, such as Petri nets and MS matrix model. Moreover, structural properties of MJI matrix offer direct insight in the system configuration, hence, providing a ground for the system analysis and supervisory controller design. Properties, such as circular waits and conflicts, can be determined straightforwardly by using simple matrix manipulations, thus, allowing design of sequencing control algorithms. An extension of MJI matrix in time domain offers a foundation for determination of recursive equation that can be used for simulation of system’s dynamics. Although manufacturing systems have been used for validation of the proposed modeling technique, the method can be applied on other discrete event systems as well.