Taking the Chongqing section of the Three Gorges Reservoir area as the research area, the changes of land use and carbon storage in this area were studied to provide some theoretical references for ecological barrier protection, future territorial spatial planning and land management in this area. Based on GlobeLand30’s three periods of land use data in 2000, 2010 and 2020, Markov and InVEST models were applied to analyze the spatio-temporal characteristics of land use change in the study area from 2000 to 2020, and carbon density databases of different land use types (hereafter referred to as land classes) were established to estimate the carbon storage of terrestrial ecosystems. The results showed that: 1) the land use structure of the study area was mainly composed of forest and cultivated land, accounting for more than 85% of the total area of the study area. From 2000 to 2020, land use transfer in the study area mainly occurred between forest, grassland, artificial surface, water body and cultivated land. The area of forest, water body and artificial surface showed a net increase, in which the artificial surface movement attitude was the highest, reaching 17.33%. The area of other land types showed a net decrease trend, and the area of cultivated land and grassland had a significant decrease. 2) From 2000 to 2020, the total carbon storage of the study area increased first and then decreased, and the transfer of cultivated land to water and artificial surface was the main factor of the decrease of total carbon storage. The transfer of cultivated land and grassland to forest was the main factor for the increase of total carbon storage. 3) In terms of space, carbon storage in the study area presents the characteristics of “high in the east and low in the west, more in the north and less in the south” and gradually decreases from the head of the reservoir to the end of the reservoir. The carbon source areas are concentrated and distributed in the downtown area of Chongqing, the surrounding areas of counties and towns, and along the Yangtze River. The carbon sinks are mainly concentrated in Qinba Mountain, Wushan Mountain, Qiyao Mountain and Fangdou Mountain. The results suggest that the ecological function of the study area has been further strengthened from 2000 to 2020, and the policies and measures of returning farmland to forest, grassland and afforestation have been effectively implemented. The transfer between high carbon density and low carbon density is the main factor of carbon storage change in the study area. The rapid encroachment of man-made surface into farmland and forests around cities and towns is an important reason for the decrease of total carbon storage in the study area from 2000 to 2020.