For flexible manufacturing systems (FMSs) with multiple unreliable resources, both deadlocks due to unreasonable resource allocations and blockings caused by the failure of unreliable resources are considered when designing controllers. Firstly, Petri nets are utilized to model the above systems, and resource transition circuits, a kind of graphical structures of Petri nets, are used to characterize the deadlocks and blockings of the systems. Then based on the concept of effective transition covers, a Petri nets controller is synthesized with small sizes and strong robustness. Finally, two examples are utilized to illustrate the effectiveness of the proposed robust controller.