In order to resolve a deadlock problem in manufacturing systems, three main methods have been proposed-prevention, avoidance, and recovery. The prevention and avoidance methods require predicting deadlocks in advance in order to prohibit them. In contrast, the recovery method allows a system to enter a deadlock state, then resolves it usually using a common buffer. In this paper, a deadlock recovery method considering the impact of flexible job routings is proposed. This method is based on capacity-designated directed graph (CDG) model representing current requesting and occupying relations between Jobs and resources in order to detect a deadlock and then recovers it.