Composition of merger and acquisition risk of agricultural manufacturing enterprises in China is analyzed, which is mainly strategic risk, external risk, transaction risk and integrated risk. And there are a total of 16 specific sources of risk. Concrete assessment methods for merger and acquisition risk of agricultural manufacturing enterprises are introduced. Firstly, set up the risk factor sets at first and second layers and divide merger and acquisition risk into 5 layers; establish risk assessment matrix according to the score by expert group. Secondly, determine the weights of the various risk factors by the ideology of information entropy. Finally, find out the subordinated vector of risk factor, construct risk assessment matrix, calculate the second grade risk assessment vector and conduct risk assessment. Taking an agricultural manufacturing enterprise as an example, fuzzy mathematics method is used to conduct risk assessment on its merger and acquisition project. Result shows that the overall risk of merger and acquisition project is relatively low, and merger and acquisition can be implemented. Merger and acquisition risk assessment based on fuzzy mathematics has made the assessment result more objective and reliable, so as to provide a reasonable reference for the scientific decision-making of agricultural manufacturing enterprises in China.