Bipolar low-voltage DC distribution networks have the advantages of renewable energy integration, flexible power supply mode and high-power supply reliability, but their short-circuit faults have a serious impact on power supply reliability. In this paper, a fault comprehensive current limiting control strategy based on a bipolar isolated modular multilevel DC transformer is proposed for unipolar grounding and bipolar short-circuit faults in bipolar low-voltage DC distribution networks, which effectively suppresses the internal overcurrent of the transformer and the output fault current by means of combining software and hardware, so as to effectively reduce the cut-off time and the capacity requirement of the DC circuit breaker. The current fault components of bipolar low-voltage DC distribution networks under different faults are analyzed, and a fault identification criterion based on the average value of the current integral is proposed, and a protection scheme for bipolar low-voltage DC distribution networks is constructed by combining with directional elements and time-delay elements. Simulation verifies the correctness and effectiveness of the comprehensive fault current limiting control strategy and protection scheme.