Combined with the actual operating situation of one fatty acid methyl ester refining and separation device in China and from the point of the physical characteristics of the fatty acid methyl ester, the design key points of the heat-sensitive material continuous distillation device in high vacuum were put forward. In addition, from the technological process design essentials, equipment selection and internals arrangement were further investigated, the design essentials of refining and separation device of fatty acid methyl ester. Finally, according to the problems encountered during the device operation, the operation cautions of this device were pointed out, an important reference was pointed out for the design of refining and separation device of the fatty acid methyl ester and the continuous distillation device of heat-sensitive material.