The Grain to Green Program (GTGP), as a policy tool for advancing ecological progress, has been operating for 20 years and has played an important role in improving ecosystem service values. However, there are few studies on the trade-off/synergy changes in ecosystem services during the implementation of the GTGP and how to select the optimal scheme for regional ecological security based on the trade-off relationship. Thus, we took the Chengdu-Chongqing urban agglomeration (CCUA) in southwestern China as the study area; we used multisource data and the corresponding models and methods to estimate the regional food production, carbon sequestration, water yield, soil conservation and habitat quality services. Then, we clarified the trade-off/synergy relationships among ecosystem services from 2000 to 2015 by spatial analysis and statistical methods and evaluated the influential mechanism of the GTGP on trade-offs between ecosystem services. Finally, different risk scenarios were constructed by the ordered weighted average algorithm (OWA), and the regional ecological security pattern was simulated under the principle of the best protection efficiency and the highest trade-off degree. We found that (1) the trade-offs/synergies of regional ecosystem services changed significantly from 2000 to 2015. Among them, food production, water yield and soil conservation have always had trade-off relationships, while carbon sequestration, soil conservation and habitat quality have all had synergistic relationships. The relationships between carbon sequestration and water yield and food production changed from non-correlated to trade-off/synergistic, and the relationship between habitat quality and food production and water yield was not obvious. (2) Except for carbon sequestration service, the trade-off intensity between other ecosystem services decreased, indicating that the change trend of ecosystem services in the same direction was obvious. (3) The GTGP has been an important factor affecting the trade-off intensity of regional ecosystem services. On the one hand, it has strengthened the synergistic relationships among carbon sequestration, soil conservation and habitat quality; on the other hand, it has increased the constraints of water resources on soil conservation and vegetation restoration. (4) The decision risk coefficient α = 1.6 was the most suitable scenario, the total amount of regional ecosystem services was high, and the allocation was balanced under this scenario. The ecological security area corresponding to this scenario was also the area with high carbon sequestration and habitat quality services. The purpose of this study was to provide a scientific reference for the precise implementation of the GTGP.