Rekeng geothermal system in Eastern Himalayan syntax is found to exhibit the strongest surface manifestations in the western Sichuan plateau, with numerous boiling springs, fumeroles and geysers. What is the heat source of such a high temperature system? Is there a magmatic heat source to support it? In this study we have attempted to seek clues from the isotope geochemistry of geothermal fluids. The stable isotope delta H-2 and delta O-18 composition of geothermal water suggests that it is recharged by precipitation and snow melt of the surrounding mountains. The chemical type of the geothermal water is alkaline HCO3-Na as a result of water-CO2-rock interaction. Geothermal reservoir temperature in the fractured metamorphic rock is estimated to be between 200 degrees C-225 degrees C, using the chemical geothermometers and the chemical thermodynamic modeling approach. During the degassing process upon rising, 0.05 mol/L CO2 has escaped from the geothermal fluid. Evidence from the relationships among major ions and geothermal suite (Li, B, F, As) indicate that the hot springs shared the same parent source fluid and they mixed with cold groundwater to different levels in the subsidiary fractures near surface. Carbon isotope signatures show that the CO2 enriched geothermal gas is 95% of crustal metamorphic origin. Additionally, based on helium isotope analysis, the mantle magmatic He-3 signatures have been largely obliterated since it accounts for no more than 5%, implying there is no underlying mantle-derived magma chamber acting as heat source. Therefore, a significant portion of heat is likely converted from crustal deformation in view of the regional tectonic background as Eastern Himalayan syntax.