The invention discloses a thermopile principle based heat flux sensor which is used for measuring surface heat flux. The heat flux sensor is of a cylindrical structure. A cylindrical base is machinedfrom a to-be-measured material. One end face of the cylindrical base is used as a measurement surface. The measurement surface is designed to be conformal to the surface shape of the to-be-measured material. The measurement surface is provided with a plurality of grooves. The grooves are filled with a special material. The filled measurement surface has the same shape with the measurement surfacebefore the grooves are arranged. A sensitive element is attached to the surface of the measurement surface. Cold joints of the sensitive component are attached to the surface of the material with higher thermal conductivity between the cylindrical base material and the special material, and heat joints are attached to the surface of the material with lower thermal conductivity. The two ends of thesensitive element are connected to output lines. The output lines are drawn through line outlet holes on the cylindrical base. According to the invention, thermal interference caused by the heat fluxsensor can be minimized, the accuracy of measurement can be improved, and the sensitivity and response speed of the heat flux sensor are significantly improved.