The centralized topology with three-level inverters are widely used in photovoltaic (PV) systems due to their less installation costs and complexity. However, the common maximum power point tracking (MPPT) is a disadvantage of the centralized topology particularly under the partial shading and panel mismatch conditions. In this system, if PV modules are separately connected to the split capacitor voltage, the MPPT efficiency can be improved by the proposed control strategy. By the proposed method, the two capacitor voltages can be controlled asymmetrically to perform the separate MPPTs of each PV module connected to separate capacitors. The outputs can be generated without distortion even if two capacitors are asymmetrically regulated. Simulation and experimental results verify the validity and feasibility of the proposed methods.