The submarine heat flow probe is a high-resolution, high-precision temperature measurement equipment, temperature calibration is carried out periodically which is an essential part to ensure the accuracy of the measurement data. The traditional temperature calibration is not applicable to Guangzhou Marine Geological Survey temperature gradient probe because of the size and other technical indicators of the submarine heat flow probes, design a calibration method based on US Seabird SBE 917plus type conductivity-temperature-depth system (CTD) which is suitable for deep-sea temperature measurement equipment. This method can be applied to check seafloor heat flow probe by sea trials, which provides a new checking method while the conventional methods can not be verified in the deep sea temperature measurement equipment. This method achieved good results in the offshore applications survey and broaden its applications, which can also be used to temperature calibration for other deep-sea temperature measurement devices.