This paper proposes a new control structure for two feeders, three phase four wire distribution systems (3P4W) operating with multi-converter unified power quality conditioner (MC-UPQC). The modified synchronous reference frame theory (MSRF) is mainly used in the new controller design. The proposed system is designed and applied for two feeders of 3P4W with UPQC. This system employed with three voltage source converter which is connected commonly to two feeder distribution systems. The proposed control scheme is simulated with 3P4W and it is efficiently compensate the voltage sag and reduce the total harmonics distortion under linear and nonlinear load conditions. The fast dynamics response of dc link capacitor is achieved with the help of Fuzzy logic controller. The neutral current flowing in series transformers of the two feeders is zero with the implementation of proposed system.