In this paper a multilevel inverter configuration is proposed for standalone photovoltaic (PV) generation system. The multilevel inverter is configured using three two level three phase inverter and three phase transformer having multiple winding in primary side with appropriate turns ratio. The three phase inverters are fed from separate PV arrays with asymmetrical voltage and power rating to distribute the total generated power among load and battery storage units. To supply major load demand one of the PV array with associated inverter (main inverter) rated relatively higher power compared to remaining two inverters. To reduce the initial cost, battery backup are provided only to remaining two arrays. The main inverter is controlled by varying the modulation index in such a way that during excess generation at the associated array in addition to supplying the load the batteries associated with other PV arrays are also charged. The topology also has additional advantage of fault tolerant capability in terms of inverter switch open circuit fault and/or source failure. The configuration is validated by using MATLAB/Simulink and a laboratory prototype for various test results with and without fault conditions are presented. © 2016 IEEE.