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In order to analyze the deadlock problem arose from the competition of tools resource in the flexible manufacturing system where the processes were non-interrupted, graph theory method was adopted and tool resource allocation graph (TRAG) was proposed. The relationship between tool flow deadlock and tool resource allocation graph (TRAG) was described after the TRAG was set up. A dynamic scheduling principle model was established. Based on this, a two-level deadlock control strategy was proposed to solve the tool-flow scheduling problem. The algorithms of deadlock detection and tool allocation were given. Analysis showed that the strategy and algorithm can avoid deadlock effectively when system is running. So the control to tool-flow deadlock and tool allocation were effectively implemented while the processes were noninterrupted.