Cave systems serve as key interfaces connecting surface and underground carbon cycles, and research on their carbon dynamics provides a unique perspective for revealing the mechanisms of carbon transport and transformation in karst critical zones. In this study, we established a multi-factor monitoring framework spanning the atmosphere–soil–cave continuum and associated meteorological conditions, continuously recorded cave microclimate parameters (temperature, relative humidity, atmospheric pressure, and cave winds) and CO
2 concentrations across atmospheric–soil–cave interfaces, and employed stable carbon isotope (δ
13C) tracing in Mahuang Cave, a typical karst cave in southwestern China, from 2019 to 2023. The results show that the seasonal amplitude of atmospheric CO
2 and its δ
13C is small, while soil–cave CO
2 and δ
13C fluctuate synchronously, exhibiting “high concentration-light isotope” signatures during the rainy season and the opposite pattern during the dry season. Cave CO
2 concentrations drop by about 29.8% every November. Soil CO
2 production rates are jointly controlled by soil temperature and volumetric water content, showing a threshold effect. The δ
13C response exhibits nonlinear behavior due to the combined effects of land-use type, vegetation cover, and soil texture. Quantitative analysis establishes atmospheric CO
2 as the dominant source in cave systems (66%), significantly exceeding soil-derived contributions (34%). At diurnal, seasonal, and annual scales, carbon-source composition, temperature and precipitation patterns, ventilation effects, and cave structure interact to control the rhythmic dynamics and spatial gradients of cave microclimate, CO
2 levels, and δ
13C signals. Our findings enhance the understanding of carbon transfer processes across the karst critical zone.
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