Aerospace thin-walled parts have the characteristics of low stiffness and complex structure, which are easily deformed by machine tool vibration, cutting force and heat during machining. The traditional fixture is in point contact with the workpiece, and the workpiece bears uneven force, which results in poor surface quality and low precision of the part. Therefore, it is urgent to improve the machining efficiency and surface quality of workpiece. According to the performance of magnetorheological fluid, a magnetorheological flexible fixture is designed to completely wrap the parts so as to make them bear uniform force, improve the stiffness of the system and inhibit flutter. Firstly, the stiffness distribution of thin-walled parts, flexible fixtures and fixture-workpiece system is studied in this paper. It can be seen that the symmetrical center stiffness of magnetorheological flexible fixtures is relatively low. Through milling experiments with single process parameters, it is found that when the rotational speed, cutting depth and feed speed change, the composite clamping effect is better than the traditional clamping effect, in which with the increase of rotational speed, the vibration acceleration in Ax, Ay and Az directions decreases by 25.16%, 26.87% and 10.78% respectively; When the cutting depth increases, Ay decreases by 23.12% at the maximum. When the feed speed changes, it decreases by 15.78%. Finally, based on the case of milling thin-walled parts with magnetorheological flexible fixture, it is obtained that the coaxiality of composite clamped thin-walled parts decreases by 13.85%, and the maximum decrease of cylindricity is 36.73%. Roughness value Rz decreases by 80.47% at the maximum. In summary, the above results have verified that the machining quality of the magnetorheological flexible fixture is better.