With the large-scale access of volatile and intermittent new energy sources, gradually increasing attention has been paid to distributed power flow controller (DPFC) technology with its cost-effectiveness and function advantages, and a number of engineering projects have been put into operation. To improve the safety and reliability of DPFC operation, combined with the structure of DPFC, this paper studies the types of faults that may occur during operation. The equivalent circuit corresponding to each fault type is constructed. Based on these, the external performance characteristics of the sub-modules of the DPFC device under fault conditions such as series coupled transformer failure, IGBT device failure, trigger signal loss/DC power supply damage, etc., are analyzed and extracted. Combining the fault phenomenon and the DPFC start-stop action timing, a protection configuration scheme for the DPFC is developed. DPFC transformer over-voltage protection, DC capacitor over-current/over-voltage protection, as well as DC capacitor voltage loss protection strategies are proposed. The electromagnetic transient model containing DPFC is completed using PSCAD/EMTDC. Simulation results show that the protection configuration and strategy proposed can satisfy the protection requirements of DPFC. This work is supported by the Technical Innovation Special Major Project of Hubei Province (No. 2019AAA016).