- Helium and neon isotopic compositions indicate that helium originates from the crust with minor addition of mantle 3He (~5%).
- Carbon isotopes reflect mixing between limestone and sedimentary sources.
- Low 3He/4He ratios result from the dilution of crustal radiogenic 4He and low-permeability fault systems.
Late Palaeozoic and Cenozoic magmatism, including Pingbian Quaternary basaltic volcanoes, occurs in southeast Yunnan, China, where seismic tomography evidence indicates magma activity in the uppermost mantle. However, the characteristics of mantle fluid release remain poorly understood. Here, we report the chemical compositions of hot spring gases in SE Yunnan and measure the 3He/4He ratios, 4He/20Ne ratios, and δ13C-values (CO2, CH4) to determine their origins and the factors influencing their migration. Except for five samples contaminated by the atmosphere (4He/20Ne ratios, 0.39 ̶2.39), the Rc/Ra ratios (Rc is the air-corrected 3He/4He ratio, Ra is the air ratio with 1.4 × 10−6) range from 0.042 Ra to 0.470 Ra, indicating that the helium is mostly of crustal origin with minor addition of mantle-derived helium. The calculated maximum proportion of mantle helium was ~5% of total helium, indicating that mantle 3He leakage correlates with the ductile lower crust. The hot spring gases are fractionated by the partial dissolution of CO2 in groundwater, and the initial δ13CCO2 values are modelled by Rayleigh fractionation within a range of −26.5‰ to −6.14‰. The modelled CO2 in samples estimated by the HeC isotope coupling model originates from the mixing of limestone and organic sediment end-members. The isotopic signature of CH4 (−69.2‰ to 35.9‰) suggests a thermogenic source and microbial oxidation in some samples. Furthermore, the apparent isotopic temperatures are estimated using fractionation factors for CH4 and CO2, suggesting a lack of magmatism in the crust beneath the Red River fault zone (188–318 °C), but partial melting under the Bozhushan granitoid plutons (572–688 °C). The low emission of mantle-derived helium is attributed to the low fault permeability and minor active crustal deformation in present-day SE Yunnan, which restrain the upward migration of mantle fluids.