An energy analysis model and several evaluation indexes are established for a novel gas separator employing molecular exchange flow as working principle. The influences of several important factors on energy consumption and thermal efficiency are investigated. As temperature difference increases, both energy consumption and thermal efficiency rise linearly. As Knudsen number increases, total work decreases while minimum separation work and thermal efficiency initially increase and subsequently decrease. When inlet velocity increases, total work increases but minimum separation work and thermal efficiency go down. Furthermore, both energy consumption and thermal efficiency initially rise and then decline with an increasing mole fraction of the lighter molecular weight component. The results indicate that energy consumption and separation performance should be taken into consideration when selecting temperature differences. In addition, it is preferable to choose the Knudsen number corresponding to optimal separation performance and the intermediate value for component mole fraction. Moreover, it had better employ a lower inlet velocity as long as the separation requirements are satisfied. This study presents a method to optimize the performance of the novel separator based on molecular exchange flow from the perspective of energy conversion and utilization.