Although karst regions account for 39% of the total area of Chongqing, there is still considerable uncertainty in the estimation of karst carbon sink flux (CSF). Additionally, the contributions of climate change and ecological restoration to the CSF in this region remain uncertain. Based on this, the spatial and temporal patterns of karst carbon sinks in Chongqing from 2003 to 2022 were estimated by the GEM-CO2 model using lithological geological data and meteorological data. We also explored the impact mechanisms of climate change and ecological restoration on CSF. From 2003 to 2022, the karst carbon sink in Chongqing exhibited a fluctuating downward trend, with a decline rate of 0.064 tC km-2 a-1. The carbon sequestration flux was 9.17 tC km-2 a-1, and the total amount was 24.09×104 tC /a. The CSF in the northern karst regions of Chongqing was higher than in the south, showing an increasing gradient from south to north. The contributions of precipitation, temperature, evapotranspiration, soil moisture, and normalized vegetation index to CSF were 38.20%, 30.88%, 14.19%, 8.37%, and 8.36%, respectively. Compared with temperature and evapotranspiration, the decrease in precipitation was the primary driver of the declining CSF flux over the past 20 years. The results of this study reveal the spatial-temporal characteristics of karst carbon sequestration and its driving factors in Chongqing, providing data support for the realization of carbon neutrality in Chongqing. Additionally, it offers valuable experience for other provinces and even countries in diagnosing carbon neutrality capacity and analyzing gaps.