The effect of global warming and the scarcity of fossil fuels has created an enormous problem in today’s era. To overcome such a problem, renewable energy sources, particularly solar energy, play a crucial role in meeting the developing need for power. However, the design of the Solar Photovoltaic (PV) system is interrupted by various factors such as the effect of temperature, isolation, aging, partial shading conditions, etc. Among all the factors mentioned, partial shading results in the significant diminution of power. To address this shading effect and enhance the flexibility of the PV system in terms of better utilization and energy extraction, a 31-Level Cascaded H-Bridge Multilevel Inverter (CHB-MLI) has been implemented to the autonomous PV system comprising of Maximum Power Point Tracking (MPPT) controller, boost converter and variable loads in MATLAB/Simulink architecture. To track maximum power from PV during varying irradiance and temperature and to further improve the system performance in terms of better convergence speed, an MPPT system with a Modified Flower Pollination Algorithm (MFPA) based PID controller has been proposed in this paper. To justify the suggested approach, the is-landed PV system is led to variation in irradiance and load. A detailed comparison of the proposed MFPA technique with classical control techniques has been meticulously discussed. The results obtained indicate that the suggested MFPA tuned PID with MLI outperforms the conventional methods in better system stability, reduced harmonics, and enhanced capacity to track maximum power from the PV system. In addition to this, the Total Harmonic Distortion (THD) using Fast Fourier Transform (FFT) has been found to verify IEEE-1547 power quality constraints. The values are found to be well within limits, thus justifying its real-time applications.