In the automated manufacturing systems, the problem regarding how to make production activities flexible is even more important and critical than that regarding how to product large quantities, and the more flexible, if possible, the manufacturing system is, the more competitiveness and profitable factors it gets. This research, therefore, concentrated on establishing the flexibility and evaluating performance on the manufacturing system, operational flexibility is considered because of enabling the manufacturing system to get both the improvement of production rate and the adaptive ability of environment changes. For it, we used the analytical tool, GSPNs, which is a kind of timed Petri-Nets. GSPNs is competent enough to consider practical situations just like operation priorities, machine failure, randomness, concurrency and so on. Through the GSPNs analysis, it is confirmed that in the manufacturing system with operational flexibility is compatible with the traditional performances such as production rate or mean waiting time.