The hybrid distribution transformer integrated photovoltaic system (HDT-PV) is a promising solution for realizing the local consumption of distributed solar energy and solving the problems of the following power quality in the active distribution network. Due to the integration of power electronic converters and photovoltaic systems with low-frequency transformers, the fault situations of the HDT-PVs are more complicated and frequent than those of conventional distribution transformers. The lack of protection strategies for the HDT-PV, a new type of power equipment, greatly reduces its reliability and limits its potential for practical applications. To address this issue, the paper proposes multi-layer protection strategies for the HDT-PVs to remove the faulty part under different possible failure conditions. For each protection strategy, the corresponding fault-tolerant control system of the HDT-PV is designed to ensure the normal operation of other functions under different fault conditions. Finally, simulation and experimental results are provided to verify the effectiveness of the proposed multi-layer fault-tolerant protection strategies for the HDT-PVs.