Many important Petri net-based methods have been presented to prevent deadlocks in automated manufacturing system with concurrent sequential processes. This paper addresses deadlock problems in automated manufacturing systems with multiple resource service. Petri net is used to model the flow of the parts and the usage and release of the resources. Deadlock structure objects in Petri net models, which lead the system to deadlock, are characterized. This paper proves that, by adding a control place for each deadlock structure so that the number of parts in the deadlock structure is limited, deadlock can be successfully prevented. Using the including relation between deadlock structures, from inside to outside, the Petri net controller is synthesized, and it is proved that the presented controller is a maximally primitive Petri net controller.