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In the current financial crisis, the business risk has been exacerbated. Mergers and acquisitions has become a hot issue. In knowledge management process of the mergers and acquisitions, Corporate concerns are about the risks of knowledge management in supply chain. This paper aims to develop a qualitative risk model with the data of Yangtze River Delta of China, to empirically identify the important risk factors of knowledge management for the supply chain logistics in mergers and acquisitions. Starting with the importance of knowledge management risks in supply chain logistics, then, paper proposed an optimization of the risk management process, a new paradigm for risk of knowledge management in supply chain planning and logistics control system is required in mergers based on risk management theory.