The proposed work mainly deals with transformer-based three-phase Multi-Level Inverter (MLI) where the switches in MLI are controlled by Multi-Carrier PWM (MC-PWM) techniques. In this article, 48V DC input voltage is fed to 48/400V High-Voltage DC-DC boost converter which is controlled by Proportional-Integral (PI) and Neural-Network (NN) tuned PI controllers. 400V DC output from boost converter is connected to three-phase MLI where the MLI switches are controlled by three different types of MC-PWM techniques like Phase Disposition (PD), Phase Opposition and Disposition (POD) and Alternate Phase Opposition and Disposition (APOD). The overall system performance in terms of Total Harmonic Distortion (%THD) is analyzed and it is depicted that the proposed system under different modulation indices gives improved THD results with an NN tuned PI controller-based boost converter. The whole analysis is performed on the MATLAB\Simulink platform.