In this paper, a measurement system for surface temperature and surface heat flux was developed to study heat transfer mechanism in boiling process. The system was consisted by two parts: (1) inner block temperatures were measured using micro-thermocouples set at two layers inside heating block; (2) with using the measured temperatures, inverse heat transfer analysis was performed to get surface heat flux and surface temperature. For the inner block temperature measurement, special T-type micro thermocouples with a common positive pole were developed. Totally 20 thermocouples were set at two layers at the depths 3.1μm and 4.905mm beneath the boiling surface, in a radius of 5mm. The developed system was used to research the change of surface heat flux and surface temperature in a boiling process. Experiments were performed to pool boiling at atmospheric pressure. The experiments showed the developed special T-type micro thermocouples could trace temperature change in boiling process successfully. With comparison to images from a high-speed camera, temperature change tendencies in boiling process were tried to understand. Then one dimensional inverse heat conduction problem was solved to get surface heat flux and surface temperature. Increase in surface heat flux with the generation of big bubble was derived successfully.