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This paper aims to update our understanding of the carbon cycle in the Himalayas, the most intense collisional orogeny globally, by providing new insight into its impact on Cenozoic climate cooling through the use of isotopic variations in both organic and inorganic carbon and an isotopic mass balance model. Our results from 20 selected hot springs show that the relative contributions of dissolved carbon from the mantle, metamorphic decarbonization, aqueous dissolution, and soil organic matter are approximately 2%, 82%, 6%, and 10%, respectively. Approximately 87% ± 5% of CO2 generated in the deep crust precipitates as calcite, while approximately 5.5% ± 1% of this carbon is converted to biomass through microbial chemosynthesis at depths less than 2 km. Our random forests approach yielded a metamorphic carbon flux from the entire Himalayan orogenic belt of approximately 2.7 ∼ 4.5 × 1012 mol/yr. The minor CO2 released into the atmosphere (2.5 ∼ 4.2 × 1011 mol/yr) is comparable to the carbon consumption driven by Himalayan weathering. This paper provides new insights into deep carbon cycling, notably that approximately 93% of deeply sourced carbon is trapped in the shallow crust, rendering orogenic processes carbon neutral and possibly acting as one of the major triggers of long‐term climate cooling in the Cenozoic. Plain Language Summary: Large‐scale deep metamorphic decarbonization and CO2 release into the atmosphere during continental collision orogenesis worldwide have had significant impacts on Cenozoic global climate change. However, the carbon sources and sinks and the mechanisms underlying their impacts on climate change are not fully understood. This paper reports the chemistry of aqueous solutions, carbon isotopic compositions of dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC), and helium and carbon isotopic compositions of free gases from hot springs in southern Tibet. The carbon isotope fractionation model between gas and aqueous solutions revealed that the carbon released from depth underwent six different stages. Based on the random forests machine learning algorithm, we estimated the metamorphic carbon flux across the Himalayan orogenic belt. Furthermore, only a small fraction (7%) of deep carbon is eventually released into the atmosphere, and this volume is the same magnitude as the amount of carbon absorbed by silicate weathering on the Tibetan Plateau. This paper emphasizes that the carbon sequestration process in the upper crust may have resulted in nearly carbon‐neutral geological bodies in the Himalayan orogenic belt, thus playing a critical role in Cenozoic climate cooling. Key Points: Approximately 87% of deeply sourced carbon precipitates as calcite, while approximately 5.5% is sequestered as biomass in the shallow crustThe carbon flux across the Himalayan orogenic belt was estimated by the random forests approachCrustal thickening has attenuated long‐term deep carbon emissions from the Himalayas [ABSTRACT FROM AUTHOR]