Flexible DC distribution system is an important development direction of future DC technology and distribution system. However, due to poor ability of power electronic equipment to withstand fault current, its protection needs to use transient information within a few milliseconds to identify fault area and, considering operation of protection based on transient unit, it is often confined by distributed line capacitance and communication error, thus resulting in a challenge. Hence, this paper proposes a new protection scheme for flexible distribution system based on cosine similarity of DC current waveform. Compared with the traditional current polarity comparison based pilot protection directly measuring current direction (positive or negative), this paper proposes cosine similarity criteria to efficiently extract the multi-band features of the transient current. The proposed method is robust to distributed capacitance, and not requires strict communication synchronization. Therefore, the proposed pilot protection has lower instrument requirements comparing with traditional transient current differential protection, and can quickly and accurately identify fault position. Simulation results show that the proposed protection scheme can identify internal faults in less than 0. 3 ms with good reliability and high sensitivity. The proposed protection scheme is feasible for industry application and relatively robust to noise and high fault resistance, enabling the communication not to be strictly synchronized, and will not be affected by distributed line capacitance. © 2019, Power System Technology Press. All right reserved.