Due to the long seed industry chain, short cycle and high technical requirements, the lack of management experience in the process of merger and integration makes the actual process of merger and integration there are a lot of merger and integration risks. The merger integration process is divided into the early stage of the mergers and acquisitions, mergers and acquisition phase of the three stages, the ISM model (explanation structure model) is used to analyze the relationships among different risk factors of merger and their structure,Some references are proposed for Beijing seed industry enterprise M&A strategy to reduce the risk of seed industry merger and integration, promote the development of Beijing seed industry.