The installation of muzzle brake changes the flow direction of propellant gas, which leads to a decline in the recoil force but an increase in the muzzle flow noise of the side rear. Therefore, the coordination between high efficiency and low harm of muzzle brake is one of the factors limiting its optimization. To address this problem, a numerical method for evaluating the comprehensive performance of muzzle brake targeting muzzle brake efficiency and impulse noise is proposed in the present study. The two performance indexes are calculated using a computational fluid dynamics (CFD)-computational aeroacoustics (CAA) coupled method. Afterwards, a corresponding experiment is conducted to verify its feasibility. Furthermore, the comprehensive performance of muzzle brakes with three different structures are analysed based on the two indexes obtained by the proposed numerical method. The results reveal that both indexes can be influenced by the structure of muzzle brakes. The increased braking efficiency is almost accompanied by increased impulse noise, but the functional relation is not linear dependence. Thus, the comprehensive performance can be improved by optimization of the structure. The evaluation method proposed in this paper has theoretical significance for optimizing muzzle brakes, which is of great engineering value.