In this paper, we propose an efficient search algorithm for finding an optimal schedule to minimize makespan, while avoiding deadlock situation in Flexible Manufacturing Systems (FMS) with finite capacity, in which each job needs to be processed in several job stages for completion. The proposed algorithm uses a modeling and control method based on Petri-net. Especially, we improve the efficiency of the search algorithm by using a priority rule and an efficient bounding function during the search procedure. The performance of the proposed algorithm is evaluated through a numerical experiment, showing that it holds considerable promise for providing an optimal solution efficiently comparing to past work.