This paper is proposed to establish an optimal control method for UPQC (Unified Power Quality Conditioner) to improve power quality and manage effectively equal power sharing between shunt and series inverter of UPQC under electrical faults condition. The UPQC is modeled to protect sensitive load from source side voltage disturbances under nonlinear load conditions. A hybrid power generator that integrates a proton exchange membrane fuel cell (PEMFC) as the main energy source and a super capacitor (SC) as secondary source is proposed to feed the FACT device. In this work, a new control strategy is presented for considering the voltage sag, power factor and total harmonic distortion (THD) as multi objective of UPQC controller. For this purpose, a new powerful algorithm named virus colony search (VCS) is used for determining the coefficients of the PI controller of UPQC. By using the fuzzification process for the objectives function, a suitable fitness function is established for the optimization method. From the simulations, it can be seen that the results obtained by the proposed algorithm are best and attractive compared to other method. Consequently, the proposed strategy is effective and outstrips other strategies. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.