The invention relates to a flexible transformer-substation-system direct current line protection method and an apparatus thereof. The method comprises the following steps of 1) based on a fault loop of a direct current fault condition, deriving a fault-current mathematical expression and then acquiring a fault current; and 2) according to electric appliance component stress and protection demands under a direct current line fault condition, determining a high speed current sudden change protection setting principle and completing flexible transformer-substation-system direct current line protection. In the invention, the method and the apparatus are not influenced by a fault type, a line length and other factors, quick-action performance of protection motion after a direct current line fault is increased, and simultaneously operation reliability of a whole system is improved. The method and the apparatus can be widely applied to the direct current power distribution network protection technology field.