In this paper we proposed a novel method that aggregates the “Functionality” and the “Equilibrium” to calculate the weight of comprehensive evaluation problem, The method calculate the weight coefficient according to the principle of “variance drive” firstly, then considering the development of the system balance with relative equilibrium coefficient to arrive at the comprehensive evaluation results of various systems. The method reflects the scientificity, impartiality and rationality. So it can avoid the phenomenon “one swallow make a summer”, which can promote the healthy development of the whole system. Finally, a numerical example was given to illustrate the effectiveness of the proposed method.