Speleothems are used as a promising proxy for high-resolution paleoclimate reconstruction. Partial pressures of CO2 (pCO2) is one of the most important factors in the processes of speleothem formation in caves. The objective of our study was to monitor the CO2 variations in the overlying soil, the cave air and the stream, and distinguish its sources and processes based on stable carbon isotopes in the Xueyu Cave system from October 2014 to February 2017. Overlying soil CO2 was influenced by soil temperature and soil moisture. The cave air pCO2 and equilibrium pCO2 in the stream water during two years showed very similar seasonal variations, fluctuating with high values in wet seasons and low values in dry seasons. The average δ13Csoil air value was −19.3 ± 0.8‰ and δ13Ccave air value was −18.8 ± 0.4‰ in November; while the average δ13Csoil air value was −23.9 ± 1.4‰ and δ13Ccave air value was −23.3 ± 0.3‰ in June. Moreover, the contribution from soil during the transitional ventilation (in November) was calculated based on the two end-members model of stable carbon isotopes. On the contrary, in wet season, cave air CO2 were mainly controlled by soil CO2 inputs. The total amount of C from stream degassing was calculated, which was higher in June than in November. High-resolution monitoring of cave air CO2 and its sources reveals the highly sensitive nature of CO2 dynamics within cave environments, and highlights its sensitivity to hydrological conditions in the cave system.