Unified Power Quality Compensators (UPQC) in load side utility system is not able to fully suppress harmonics in power grid and distortion in the interface system. To enhance the operation of the UPQC, a Fuzzy based Modified Universal power quality conditioning system (Fuzzy-MUPQCS) is developed. Modified Universal power quality conditioning system (MUPQCS) is a combination of two active filters in series and one active filter in shunt. A 3ϕ voltage source inverter is also used to maintain a common DC link capacitor voltage through Photo voltaic (PV) system connected to a utility grid. Highest Power Point Tracking (HPPT) algorithm is mainly used to pull out the maximum amount of power in the PV system. In this paper, Proportional integral controller based MUPQCS (PI- MUPQCS) and Fuzzy-MUPQCS are used to analyse the load voltage and load current distortion, THD analysis, power factor measurement, grid voltage and grid current distortion in the three phase system under nonlinear load conditions. The execution of the MUPQCS based 3ϕ system and the controllers are simulated using Matlab /Simulink model. © 2021 Institute of Physics Publishing. All rights reserved.