Current estimates of gross carbon flux tend to ignore the downwelling flux of CO₂ from the stratosphere. Observations showed that there is a phase shift between the time series for the concentration of the standard isotopologue C¹⁶O¹⁶O and C¹⁶O¹⁸O at Waliguan, China (36°17′N, 100°54′E, 3816 m) and several other places. Previous attempts to explain the shift have not been satisfactory. Here we show that the phase shift could be explained by the downwelling air from the stratosphere, and demonstrate that this source of CO₂ provides a useful tool for constraining the carbon cycle. Using O₃ as a proxy of stratosphere-troposphere exchange, we find excellent correlation between O₃ and C¹⁶O¹⁸O observed at the Waliguan Observatory. The observed variability of C¹⁶O¹⁸O is consistent with model predictions, thus supporting that the surface air has significant contributions from the stratosphere. Quantitative modeling may provide a powerful tool for constraining the sources and sinks of CO₂ using the isotopically enriched CO₂ from the stratosphere as a tracer.