Concentrations of helium isotopes were measured in gas and water samples from 28 thermal mineral springs in Tuva and adjacent regions of Buryatia and Gorny Altai. It is shown that fluids from 16 springs are rich in mantle helium (4–35%). With regard to the air contamination of the samples, the corrected ratios of helium isotopes (Rcor = 3He/4He) in these springs vary from 5.3 × 10–8 to 422 × 10–8. Using these Rcor values, we estimated the heat flow; these estimates were then applied to calculate the deep-level temperatures and thickness of thermal lithosphere. According to these parameters, the Tuva region is divided into two parts. Eastern Tuva (from ~96° E to the boundary with Buryatia) is characterized by abnormal helium isotope ratios and heat flow indicating the intense heating of the Earth’s crust in eastern Tuva: At a depth of 50 km, a temperature reaches 1000–1200 °C, and the thickness of thermal lithosphere is reduced to 70–50 km. This testifies to a rift process west (probably, up to 96° E) of the Baikal Rift Zone. In western Tuva, the average heat flow is much lower, ~45–50 mW/m2, which is commensurate with that in the Altai–Sayan folded area as a whole. The deep-level temperatures here are twice lower, and the lithosphere thickness increases to 150 km.