Flexible DC systems are characterized by low damping and low inertia, which may lead to potential fast fault propagation under DC faults. Due to the series connection of the embedded DC power flow controller (eDCPFC) in the host MMC, it vulnerable to the abnormal conditions. However, the device also has the capability to achieve the short-circuit fault current active suppression. To effectively limit the fault current in the meshed flexible DC transmission system and improve the safety of the device, this paper proposes a fault current limitation and self-protection control strategy for the eDCPFC. First, the fault current loop of the DC system with a multiport eDCPFC is analyzed. The detailed analysis of the fault characteristics is demonstrated through a simplified single-phase equivalent circuit. Finally, a simulation model of the four-terminal meshed DC system with a multiport embedded DC power flow controller is constructed in MATLAB/Simulink. Based on the simulation, the equivalent circuit and the fault protection strategy are verified, and the influence of the submodule capacitance parameters on the fault current limiting capability is investigated.