There is about 100 million m3 underground thermal resource storage in Chongqing, of which 75% are stockpiled in metropolitan area. 20 samples from 13 hot springs in Chongqing metropolitan area are collected and analyzed for chemistry and isotopes of heavy hydrogen, oxygen and sulfur. The results shows that these hot springs are SO2-4-Ca and SO2-4-Ca-Mg, and the water sources is precipitation. The value of δ18O is between -7.41‰~-9.48‰, which can ascertain that the recharge area of these hot springs are the karst area in these anticlines and the karst area at the north of these anticlines with the altitude of 672~1 503 m. There is a good positive correlation between SO2-4 and Ca2＋, Mg2＋. The δ34S value of the samples is between 31.46‰~34.32‰, precisely the same with the δ34S value in gypsum at the second phase of Jialingjiang formation in Early Trias. Both of them shows that rainflow and surface flow along the karst fissures infiltrate into the Jialingjiang Formation which have gypsum, and it also shows that the hot springs storage formation may be the second phase of Jialingjiang formation in Early Trias.