In view of the financing situation and problems of various sub sectors of the medical and health industry, a health industry project risk prediction scheme based on FCE algorithm is proposed. Taking the venture capital project of a large health industrial park as an example, we established corresponding risk index system from the characteristics of the health industry. Then, through the study of nonlinear evaluation model, the calculation process of FCE in project evaluation is changed. According to the establishment of specific fuzzy matrix, the computation of index weight and the output of comprehensive weight evaluation results, the final ranking of influencing index factors is obtained, to determine the risk structure of health industry projects. Finally, based on the composition and causes of each risk prediction, this paper puts forward countermeasures and suggestions to strengthen the risk management and innovate the financing mode of the medical and health industry.