In flexible job shop scheduling, two problems are studied,which are the redundancy scheduling sequence constraint among procedures and the multi-mode processing between procedures and devices. Therefore, a scheduling algorithm for flexible job shop based on pruning and layering is proposed. The algorithm first uses the directed acyclic graph(DAG) to represent the procedures and the scheduling sequence constraints among procedures, the pruning strategy to eliminate the redundant in the DAG, and the layering strategy to layer the nodes in the DAG. Then the processing mode of procedures is classified, and the procedure-device booking strategy and procedure-device pre-allocation strategy are designed. Finally, by using the event-driven scheduling strategy, at the driver moment. The procedure is scheduled according to the proposed flexible processing strategy. Theoretical analysis and practical examples proves that the proposed algorithm has a better result.