The integrated design mainly focuses on power quality (PQ) issues due to the non-linear load condition. Hence this paper proposes the grey wolf optimization (GWO) with unified power quality conditioner (UPQC) to solve the PQ problems in HRES system. The UPQC performance is increased by fractional order proportional integral derivative (FOPID) with GWO. The obtained results indicate that the proposed GWO algorithm has many advantages in various aspects such as early convergence and obtaining optimized fitness value compared to other algorithms like biogeography based optimization (BBO), genetic algorithm (GA), genetic search algorithm (GSA) with existing PI controller. The proposed system is implemented in MATLAB/Simulink platform to validatethe performance during voltage sag, current sag, real power, reactive power and in terms of total harmonic distortions (THD’s).