Partial pressure of CO₂ (pCO₂) in water column was an importamt indicator for the geochemical characteristics of carbon. Diel samples for pCO₂ and other environmental factors, i. e. pH, DO and water temperature, was taken from Gaoyang backwater area in the Pengxi (Xiaojiang) River, Three Gorges Reservoir in every 6 h. Results showed that in stable metaliminon, vertical pCO₂ increased along with the water depth. Mean value of the pCO₂ at 0.5 m depth was 152 ± 71 μatm, while that of pCO₂ at 10.0 m depth was 4568 ± 1089 μatm. Significant negative correlations between pCO₂ and pH, DO, water temperature were detected, indicating metabolism of microbial and planktonic community and penetrative convection were impacted by water temperature that regulated the distribution of pCO₂. Estimation of the water-air flux of CO₂ indicated that the general characteristic of carbon sink in the Gaoyang backwater area was obvious. A maximum sink flux of -0.33 mmol/(m²·h) was detected in 15:00 while a minimum sink flux of -0.17 mmol/(m²·h) was also detected in 3:00 of the next day.