The main circuit topology and operation principle of MMC based power electronic transformer were introduced. The corresponding fault measurement points and protection methods were also provided for the types of faults that may occur. The special faults and protections in the MMC based power electronic transformer were analyzed in detail, including the impact of the selected grounding resistance on AC input side grounding fault and DC side single pole grounding fault, the overvoltage generated by clamp dual sub module with the DC fault current suppression capability instead of the half bridge sub module after the DC pole to pole short-circuit fault occurred, and the rapidly discharging problem caused by a series of capacitors in the isolated stage of power electronic transformer. In view of the above problems, the corresponding protection strategies were put forward, and the correctness and effectiveness of the proposed method were proved by PSCAD simulation.