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Command mechanism is an indispensable component of emergency mechanism. The rational Command Mechanism is helpful to ensure the good effect and efficiency of emergency management. Mechanism design has been complete and feasible in economic analysis field, while the design of emergency mechanism is still lacking in previous study. This paper introduces the basic concepts and classification of command mechanism. Based on the detailed analysis of command systems and its effective task chain, Emergency Command Mechanism is designed on Computational Organization Theory. Besides, the evaluation and failure analysis of Command Mechanism is discussed briefly. The command mechanism in general natural disasters (such as hurricane, earthquake and tsunami etc.) is demonstrated by a case study.