Southwest China, a global biodiversity hotspot, plays a vital role in carbon sequestration and ecological restoration through its forest ecosystems. This study systematically evaluated changes in carbon stocks and their driving factors in Pinus kesiya forests in southwestern Yunnan Province, before and after the implementation of the Grain for Green Programme (GFGP) from 1999 to 2016. The research combined remote sensing technology, geographic information systems (GIS), and field surveys to achieve a comprehensive analysis. The results indicated that the GFGP significantly increased both the area and carbon stocks of Pinus kesiya forests, adding 15.97 TgC to the carbon stock, with an error margin of 4.84 TgC. This increase was primarily driven by the conversion of shrubland and farmland. Forest age emerged as a key factor influencing carbon density, which increased significantly at a rate of 4.24 Mg/ha per year. Furthermore, carbon stock distribution varied notably across different slopes and elevations, with the greatest increases observed on slopes greater than 6° and at elevations between 1000 and 1600 meters. This study innovatively integrated forest age data into land use and cover change analyses, improving the accuracy of regional carbon stock estimates. The findings highlight the GFGP’s effectiveness in promoting regional carbon sequestration and enhancing ecosystem services. However, future policies should focus on planting mixed-species forests to further enhance biodiversity. This research provides valuable scientific evidence for optimizing ecological restoration policies and offers a reference for similar restoration projects worldwide.