A new control strategy for megawatt scale series connected multilevel photovoltaic (PV) inverters is proposed. The proposed strategy ensures balanced operation under partial shading. Further under transient grid conditions such as low voltage ride through (LVRT) it is shown that the system remains connected and is fully controllable. In the proposed system, the PV arrays are grouped into zones and each zone is connected to a DC-AC-AC converter. The DC to AC inverters of multiple zones are connected in series to form the required medium voltage and transfer power to the grid. When all zones are uniformly illuminated, the output voltages magnitudes and phases of all the inverters are equal. When the insolation is different for some of the zones, the output voltage magnitude and phase angles of individual DC to AC inverters need to be adjusted in such a way that the real power from the maximum power point calculation is transferred to the grid and the power factor of the overall system is high. Also, when the grid experiences voltage sags, the system is shown to perform a low voltage ride-through (LVRT) algorithm to stay connected to the grid, without a surge in the output current. A control strategy is developed to operate the series connected multilevel inverter configuration under partial shading, by continuously monitoring the real and reactive powers supplied by each inverter. This does not employ a central controller and/or communications between the various DC to AC inverter blocks. The proposed control strategy is simulated for a 6.6 kV, three phase utility scale PV system rated at 5 MW.