This paper proposes a new control structure for two multilevel three-phase inverter topologies for photovoltaic (PV) systems connected to the grid. This control scheme includes the use of the space vector pulse wide modulation (SVPWM) technique to control the Diode Clamped Inverter (DCI) and cascade inverter topologies and the integration of the particle swarm optimisation (PSO) technique to operate the PV system at the Maximum Power Point (MPP). A Field-Programmable Gate Array (FPGA) implementation of PSO based Maximum Power Point Tracking (MPPT) is proposed to overcome the problem of MPP tracking under partial shading conditions. This MPPT technique is validated under various PV array configurations in order to evaluate the behaviour of each PV configuration under non-uniform irradiance. A SVPWM control strategy is used in order to generate gate control signals for the inverter and implemented for both DCI and cascade inverter topologies. Then, a comparative study of photovoltaic systems with these inverter topologies is carried out in the Matlab/Simulink environment and evaluated on the basis of MPPT, harmonic distortion, cost, advantages, and disadvantages. In order to test the practical implementation of the proposed control structure, FPGA/Simulink-based Hardware in the Loop approach has been used to bring the obtained results as close as possible to reality and with a minimum of constraints. Based on the analysis of the obtained results, some experimental parameters are summarized and a comparison table is obtained.