The invention relates to a low temperature heat pipe heat exchanger with a separation type micro-channel and a usage method thereof. The heat exchanger comprises an evaporation section, a middle section and a condensation section, and the middle section is positioned between the evaporation section and the condensation section. The evaporation section is connected with the condensation section through a main pipe, and thus a circular loop is formed. Micro-channel branch pipes are arranged in the evaporation section and the condensation section, and the micro-channel branch pipes communicate with the main pipe. A refrigerating medium feeding opening is formed in the middle section, the feeding opening is connected with the main pipe, and a one-way non-return valve is further arranged on the main pipe. The low temperature heat pipe heat exchanger with the separation type micro-channel has the advantages of being simple in structure, reasonable in design, high in automation degree, lower in production and maintenance costs, reliable and safe in performance and operation, capable of being widely applied and popularized and the like.