The invention provides a modular multi-level multi-terminal flexible direct current system direct current fault handling method which comprises the following steps that (1) a relay protection device detects a multi-terminal flexible direct current system in real time, if a direct current fault point is detected, breakers at two ends of a direct current line are switched off, and converters of stations are kept in a running state; (2) the switched-off breakers are switched on, whether the fault disappears is detected, if the fault does not disappear, the breakers are switched off again, and if the fault disappears, a step (3) is carried out; (3) the direct current line is used, and the system runs normally. The modular multi-level multi-terminal flexible direct current system direct current fault handling method is simple, easy to implement and reliable, influences on a plurality of converter stations of temporary direct current faults are reduced, timely recovery and running of the system after the temporary direct current faults are removed are guaranteed effectively, and device running safety is guaranteed at the same time.