Geochemical monitoring of groundwater and soil gas emission pointed out precursor and/or coseismic anomalies of noble gases associated with earthquakes, but there was lack of plausible physico-chemical basis. A laboratory experiment of rock fracturing and noble gas emission was conducted, but there is no quantitative connection between the laboratory results and observation in field. We report here deep groundwater helium anomalies related to the 2016 Kumamoto earthquake, which is an inland crustal earthquake with a strike-slip fault and a shallow hypocenter (10 km depth) close to highly populated areas in Southwest Japan. The observed helium isotope changes, soon after the earthquake, are quantitatively coupled with volumetric strain changes estimated from a fault model, which can be explained by experimental studies of helium degassing during compressional loading of rock samples. Groundwater helium is considered as an effective strain gauge. This suggests the first quantitative linkage between geochemical and seismological observations and may open the possibility to develop a new monitoring system to detect a possible strain change prior to a hazardous earthquake in regions where conventional borehole strain meter is not available.