The scientific rationality of the enterprise performance appraisal system determines the enterprise’s long-term development. In this paper, the variables and strain variables of the marginal utility function are analyzed, the morphological characteristics of the function curve are studied, an enterprise performance appraisal system is established based on the marginal utility function, and the appraisal system is solved by introducing Lagrange multipliers. Then, the performance appraisal method based on marginal utility was applied to enterprise A, and the performance appraisal index system was set up and compared by comparing it with the existing performance appraisal method of enterprise A. In terms of scientificity, 9.90% more than the original agreed that the scientificity of this method is very high, and 6.96% more than the original agreed that the scientificity is high. Regarding fairness, 15.74% more people agreed that this method is fair, and 1.05% more agreed that it is fairer. Regarding motivational effect, 7.06% more than the original agreed that this method has a strong motivational effect. The performance appraisal method based on the marginal utility function can provide a comprehensive assessment and positive guidance to employees, which provides a reference for enterprises to optimize their performance appraisal system.