Abstract: It is of theoretical and practical significance to explore the spatial and temporal changes of carbon stocks in regional terrestrial ecosystems over long periods of time and their influencing factors to achieve the carbon neutrality goal. This study couples the PLUS-InVEST-Geodector model to investigate the spatial and temporal changes of carbon stocks in the Three Gorges Reservoir Area under different scenarios from 1990 to 2035, and to quantitatively reveal the attribution factors affecting the changes of carbon stocks from the perspectives of land use changes and natural-socio-economic complex relationships. The results show that (1) the carbon stock in the Three Gorges Reservoir Area shows a fluctuation of “decrease-increase-decrease” from 1990 to 2020, with an overall decrease of 6.66 Tg, or 1.25%, among which a large area of arable land is transferred to construction land as the main reason for the decrease of carbon stock; (2) The spatial distribution of carbon stocks in the Three Gorges Reservoir Area from 1990 to 2035 is highly consistent with land use changes, and its spatial heterogeneity is significant, showing the distribution characteristics of “high in the east and low in the west, low in the south and high in the north, and head of the reservoir > belly of the reservoir > tail of the reservoir”. (3) The carbon storage of the natural development scenario and the ecological protection scenario in 2035 will be reduced by 7.53 Tg and 0.37 Tg respectively compared with the year 2020, and the ecological protection scenario can significantly reduce the carbon storage loss in the reservoir area compared with the natural development scenario; (4) The factors affecting the spatial and temporal changes of carbon storage are significant, among which land use change is the dominant factor, followed by temperature, population density, elevation and soil type, and the interaction of all factors increases the explanatory power of carbon storage changes. This study can provide scientific reference for the management of carbon pools in the reservoir area and the sustainable development of carbon storage function.