The conventional financial performance evaluation method of medical device enterprises mainly uses the Delphi feedback anonymous correspondence method to obtain the difference evaluation indicators, which is vulnerable to the impact of quantitative group decision-making factors, resulting in the low fitting of the evaluation index. Therefore, a new financial performance evaluation method of medical device enterprises needs to be designed based on the improved decision tree algorithm. That is, the financial performance evaluation indicators of medical device enterprises are selected, being able to provide objective quantitative data to help enterprises understand and measure their financial condition, risk level, and operational effectiveness, and the financial performance evaluation system of medical device enterprises is designed based on the improved decision tree, covering multiple evaluation indicators and factors, it can provide a comprehensive evaluation of the financial performance of the enterprise, so as to achieve the financial performance evaluation of medical device enterprises. The case analysis results show that the evaluation index of the financial performance evaluation method of medical device enterprises designed based on the improved decision tree algorithm has a high degree of fit, which proves that the evaluation effect of the financial performance evaluation method of medical device enterprises designed based on the improved decision tree algorithm is good, reliable, and has certain application value. It has made certain contributions to reducing the financial risk of medical device enterprises.