In order to estimate carbon storage and investigate its influencing factors in typical karst rocky desertification regions, Jianshui County, located in the upper reaches of the Yangtze River and within the Nanpan River Basin, was selected for study due to its significant ecological position. Data from Landsat 5 Collection 1 Tier 1 Surface Reflectance, Landsat 8 Collection 1 Tier 1 Surface Reflectance, and digital elevation model (DEM) were used to conduct the analysis. The google earth engine (GEE) platform and the integrated valuation of ecosystem services and trade-offs (InVEST) model was used to estimate and predict carbon storage, while the geodetector tool was employed to analyze influencing factors. The results show that, between 2000 and 2020, Jianshui County was predominantly classified as potential rocky desertification and non-desertification, with the rocky desertification area found to have decreased by 115 km² overall, and the non-desertification area increased by 21 km², reflecting an improvement in desertification conditions. Carbon storage displayed a spatial distribution pattern of "higher in the north and south, lower in the center," with recorded values of 116.293 t, 113.310 t, and 118.363 t in 2000, 2010, and 2020, respectively, demonstrating an initial decrease followed by an increase. Projections suggest that carbon storage may reach 129.981 t by 2030. Temperature (q=0.672) was identified as the primary factor affecting changes in carbon storage, with the interactions between factors shown to have a stronger effect on carbon storage than individual factors, especially the interaction between slope and temperature (q = 0.998), indicating a non-linear enhancement. It is concluded that carbon storage in Jianshui County exhibits a trend of initial decrease followed by increase, influenced by both natural and social factors, with a spatial pattern of "higher in the north and south, lower in the center."