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Travertines formed of crystalline crust have been widely reported, but there has not been focus on their geochemical characteristics. We therefore carefully conducted a series of geochemical investigations and U-Th dating on a travertine mound mainly composed of crystalline crust from Sobcha (southwest China) to determine their geochemical features and geological implications. The Sobcha travertines dominantly consist of granular crystals and fan crystals and show δ13C from 3.4‰ to 4.9‰ V-PDB, δ18O from −26.7‰ to −23.7‰ V-PDB, and 87Sr/86Sr from 0.712458 to 0.712951. When normalized to PASS, the Sobcha travertines exhibit MREE enrichment relative to HREE and LREE, HREE enrichment relative to LREE, and positive Eu anomalies. The δ13C signatures and mother CO2 evaluation of the Sobcha travertines show that the Sobcha travertines were thermogene travertines largely receiving mother CO2 from (upper) mantle (i.e., magmatic CO2) or a mixture of soil-derived CO2 and CO2 related to carbonate decarbonation. The 87Sr/86Sr of the Sobcha travertines is out of the 87Sr/86Sr ranges of local deposits exposed at Sobcha and surrounding areas but is well matched with the mean 87Sr/86Sr of Nadi Kangri volcanic rocks which cropped out to the northeast of the studied travertines (over 20 km away). This might indicate the important role of the Nadi Kangri volcanic rocks in suppling Sr to the studied travertines, but more studies are required. The LREE depletion compared to MREE and HREE in the Sobcha travertines was interpreted to be caused by the difference in geochemical mobility between LREEs and HREEs during water–rock interaction at depth, while the MREE enrichment compared to HREE was considered to be most likely inherited from reservoir/aquifer rocks. The positive Eu anomalies of the Sobcha travertines may result from very high reservoir temperatures and/or preferential dissolution of Eu-rich minerals/rocks (especially plagioclase). The Sobcha travertine mounds displays no or very slight vertical variations in δ13C, 87Sr/86Sr, and REE patterns, indicating the compositional stability of mother CO2 and paleo-fluids. However, a significant vertical increase in δ18O was observed and was explained as the result of gradual water temperature decrease related to climate cooling, self-closure of the vents, or mound vertical growth. The findings in this study might help us better understand the deposition of crystalline crust in Ca2+-deficient hot spring systems.