Control strategy of a novel multi-level converter with multi-winding MFT/HFT isolation is proposed where a medium frequency or high frequency multi-winding transformer is applied to realize the isolation and energy balance instead of conventional phase-shifting transformer. Load powers can be equalized among different windings by the energy delivery using transformer flux. The application of the proposed converter is high power locomotive traction systems, marine driving, wind power generation systems and highvoltage direct current (HVDC) transmission systems. General analysis of multi-winding isolation units is made including power characteristics of general phase shift control, analysis of other two phase shift method as well as the decoupling method of multi-winding powers. Power balancing of the isolation units is realized. Control strategy for cascaded H-bridge rectifier is put forward. Moreover, a four-step pre-charging method is proposed for this topology. Simulation and experimental results are given to validate the proposed strategy.