Aiming at the uncertainty of equipment operational effectiveness evaluation, a new method combining grey relational analysis and set pair analysis is proposed. By mining the influence of each parameter on the macro level on the uncertainty coefficient on the micro level in the expression of connection degree, the gray relational analysis method is used to determine the value of the coefficient of difference degree in its degree of freedom, so as to further reduce the influence of uncertainty in the evaluation of equipment operational effectiveness; The method is tested by evaluating and comparing the operational effectiveness of four air defense missile systems. The results show that the method is clear in concept, simple and easy to implement, and has high reliability, which provides a new idea for equipment operational effectiveness evaluation.