There are 30 carbonate hot springs in Yaoshuitan geothermal field, Xining Basin, China, with a temperature of 18~41.5 °C; and there are 10 carbonate hot springs in Qijiachuan geothermal field, with a temperature of 10~19.5 °C. Both geothermal fields are carbonate hot springs containing large amounts of CO2 gas. In order to reveal the origin of the carbonated hot springs in Yaoshuitan and Qijiachuan of Xining Basin, this paper offers a comprehensive study of the regional deep geology, tectonic setting, total analysis of carbonated hot springs, δ2H, δ18O, δ13C isotopes, main gas composition, and geochemical characteristics of travertine dating, travertine δ13C, and rare earth elements. The geological process of carbonated hot spring formation and the evolution of H+ content from deep to shallow is revealed, and the genetic mechanism of the carbonated hot spring in Xining Basin is systematically summarized. The results show that: (1) The characteristics of δ2H and δ18O isotopes indicate that the recharge source of carbonated thermal water springs in Xining Basin is mainly atmospheric precipitation. The age of carbonated thermal water springs at 14C is more than 20 ka, indicating that some of them may come from deep fluid (gas) sources. The R/Ra in carbonated thermal water springs is mostly less than 1, indicating that the helium in geothermal water is mainly crustal source helium, and there is no deep mantle source material. (2) The Piper three-plot indicates that the direction of groundwater evolution from the recharge area at the edge of Xining Basin to Yaoshuitan and Qijiachuan carbonated thermal water spring area near the edge of the basin is opposite to the normal path of groundwater evolution in the basin, which is due to the large amount of CO2 gas mixed in the deep fault along the northern margin of Laji Mountain. The ratio of (Ca2+ + Mg2+) and (HCO3− + SO42−) in the Potan and Qijiachuan carbonated thermal water springs is close to 1, and the ratio of (Na+ + K+)/HCO3− is less than 1. It indicates that the chemical composition of the Yaoshuitan carbonated thermal water spring and the Qijiachuan carbonated thermal water spring in Xining Basin is dominated by the dissolution of calcite, dolomite, and gypsum in deep carbonate reservoirs, supplemented by the dissolution of silicate minerals. The relationship between the volume fraction of CO2 and the δ13C value of carbon isotope of CO2 indicates that the source of CO2 is inorganic, which is mainly formed by metamorphism and decomposition of deep carbonate and marble. The δEu < 1 and δCe > 1 of the rare earth elements in the calcium center of the carbonated thermal water springs indicate that the groundwater supplying the travertine material has been in the acidic environment receiving CO2 from the deep crust for a long time. (3) A series of tectonic activities, such as late collision and post-collision between the Indian and Eurasian plates, has led to the uplift, asthenosphere upwelling, and thermal invasion of the northern Tibetan Plateau and other deep dynamic processes. The deep faults in the northern margin of the Laji Mountain and other deep faults with obvious neotectonic activity have provided channels for the up-invasion of deep thermal materials, and local geothermal anomalies were formed near the deep faults. The hidden carbonate rocks and silicate rocks with large thickness undergo thermal metamorphism under high temperature and high pressure in the deep geothermal anomaly area and form a large amount of CO2, which is dissolved in water and enhances the acidity of water. At the same time, the dissolution reaction of acidic water to carbonate rocks consumes H+, which keeps the carbonated thermal water spring weakly acidic. (4) The composition of travertine in carbonated thermal water springs is dominated by calcite, indicating that travertine may be formed in a deep geological environment with a temperature of 150~200 °C, indicating that there are abnormal heat sources in shallow carbonate strata with a burial depth of 3000~4000 m. The abnormal heat source may be caused by the deep fault in the northern margin of Laji Mountain, as well as other deep and large faults channeled in the deep crust and mantle heat source, indicating that the deep fault in the northern margin of Laji Mountain has an obvious heat-controlling effect, and there is a good prospect of geothermal resources exploration near the fault.