The analysis of the cyclic scheduling problem in FMS using the transitive matrix has been proposed. Since the transitive matrix may explain all the relations between the places and transitions, we propose an algorithm to get good solution after slicing off some subnets from the original net based on machines operations. For analyzing the schedule problem, we considered two time functions such as produce time and waiting time using the P-invariant. In addition, we are shown the effectiveness of proposed algorithm after comparing with unfolding algorithms.