In order to expand the evaluation system of the power plant’s cooling and ventilation flight test, and quantitatively assess the comprehensive performance level of the cooling and ventilation system under conditions of missing temperature measurement data in the engine nacelle during flight tests, the concept of integrated nacelle temperature margin is introduced, and research on a comprehensive performance evaluation method for cooling and ventilation suitable for incomplete flight test data is made. The K-means clustering algorithm is utilized for making the discretization of nacelle temperature data, and determining the weight of nacelle temperature indicators in combination with the limited tolerance relation of rough set theory. A comprehensive performance evaluation method for cooling and ventilation of engine nacelle is established and the algorithm is applied to a three-engine helicopter. The factors to influence the comprehensive performance of the cooling and ventilation system are evaluated. The results show that the changes of technical state and the engine position have great influence on the integrated nacelle temperature margin, and the maximum difference reaches 65.5 ℃ and 83.2 ℃.The integrated nacelle temperature margin can characterize the comprehensive performance of cooling and ventilation. And this method is universal, and can be used as a supplement to the traditional evaluation method of cooling and ventilation flight tests.