In order to improve the convergence and accuracy of M&A risk assessment method, an M&A risk assessment method based on adaptive immune genetic algorithm is proposed. The risk of M&A is divided into M&A preparation stage, M&A implementation stage, and M&A integration stage. The event tree analysis method is used to clarify the inducement of M&A risk events. We optimize the traditional genetic algorithm, design adaptive immune genetic algorithm to ensure the convergence of risk assessment algorithm, select the risk assessment indicators of enterprise M&A, determine the weight of the assessment indicators, and construct the quantitative model of enterprise M&A risk assessment. The experimental results show that the proposed risk assessment method takes less time, has higher accuracy, and has less probability of enterprise data imbalance.