In the hybrid modular multilevel converter (MMC) based high voltage direct current (HVDC) systems, the fault current can be actively suppressed by the converter itself, which endows a smaller requirement for current-limiting reactors (CLR) and a larger time margin for fault detection algorithms, comparing with the half-bridge MMC. But the robustness to fault resistance and noise disturbance of existing boundary protection schemes will be deteriorated with small CLRs. Moreover, the fast response of the fault current-limiting control will change the output DC voltage of hybrid MMC, which affects the fault characteristics and may cause mal-operation of existing protection algorithms. Thus, a single-end protection scheme considering the impacts of the active current-limiting control is proposed for the hybrid MMC based DC grids. The travelingwave characteristics under different fault stages are analyzed to evaluate the impacts of the fault current-limiting control. In addition, a coordination protection strategy versus different fault conditions is adopted to improve reliability. Various cases in PSCAD/EMTDC are simulated to verify that the proposed method is robust to fault resistance, fault distance, power reversal, AC faults, and immune to noise.