The reaction of hydrogen-terminated Si(100) surfaces with water during heating is analyzed using a combination of heating and cooling in thermal desorption spectroscopy. The reaction of the Si surface with water after hydrogen desorption is observed even at about 400°C at a low concentration of water molecules. An estimation method of surface hydrogen coverage by the combined measurement is proposed and the surface coverage as a function of temperature is estimated for quantitative understanding of hydrogen desorption and the subsequent reaction during heating. The combined measurement in thermal desorption spectroscopy is useful for revealing the reaction after hydrogen desorption during heating and for estimating the surface coverage.