With the acceleration of urbanization, the phenomenon of hollowing out in rural settlements has become increasingly prominent, posing significant impacts on regional ecological and food security. This study aims to analyze the impact of changes in rural settlements on ecosystem carbon storage. Using the Yangtze River Economic Belt as a case study, this paper utilizes multi-source remote sensing data and panel statistical data. Based on the INVEST model, it quantitatively analyzes the impact of changes in rural residential areas on ecosystem carbon storage since 1990. Additionally, the PLUS model is used to further simulate the future orderly withdrawal of rural residential areas and its impact on regional ecosystem carbon storage. (1) From 1990 to 2020, the Yangtze River Economic Belt exhibited a typical "decreasing population and increasing land" phenomenon, with a continuous decrease in rural population but a 26.50% increase in rural residential area, 83.55% of which was due to encroachment on arable land. (2) Between 1990 and 2020, the expansion of rural residential areas in the Yangtze River Economic Belt resulted in a total carbon storage loss of 107.87 Mt, with the encroachment of cultivated land accounting for 78.43% of the carbon storage decrease, forest land 15.34%, grassland 5.17%, and water bodies 0.99%. The encroachment of cultivated land led to a reduction of 131.87 Mt in regional ecosystem carbon storage (87.60%), followed by the encroachment of forest land (14.37 Mt, 9.60%), grassland (1.70%), and water bodies (1.10%). (3) In the future, the orderly withdrawal of rural residential areas could release 0.70×104 km2, leading to an increase of 20.18 Mt in carbon storage. The primary restoration would be to cultivated land (0.28×104 km2), increasing carbon storage by 12.48 Mt, followed by forest land (0.08×104 km2) and grassland (0.01×104 km2), contributing 4.71 Mt and 0.43 Mt respectively. [Conclusion]The orderly withdrawal from rural settlements can alleviate the pressure of decreasing arable land caused by urbanization. Through effective land resource management, it is possible to achieve dual security of rural ecological benefits and food production.