Understanding the synergic relationship between the Grain for Green Program (GGP) and the agricultural eco-economic system is important for designing an optimized agricultural eco-economic system and developing a highly efficient structure of an agricultural industry chain and a resource chain. This study used Ansai County time series data from 1995 to 2014, applied vector autoregressive (VAR) models and used tools such as Granger causality, impulse response analysis and variance decomposition, to explore the synergy between the GGP and the agricultural eco-economic system. The results revealed a synergic and reciprocal relationship between the GGP and the agroeconomic system. The contribution of the GGP to the agroecosystem reached 34%, which was significantly higher than either its largest contribution to the agroeconomic system (20.8%) or its peak contribution to the agrosocial system (26.7%). The agroeconomic system had the most prominent influence on the GGP, with a year-round stable contribution of up to 55.3%. These results were consistent with reality. However, the impact of the GGP on the agricultural eco-economic system was weaker than the effect of the agricultural eco-economic system on the GGP. The lag of variable stationarity after the shock was relatively short, indicating that optimal coupling had not formed between the GGP and the agricultural eco-economic system. On the basis of enhancing the ecological functions, we should construct the agricultural industry-resource chain such that it focuses on promoting the effective utilization of resources in the region. In addition, the development of a carbon sink industry can be used to manifest the ecological values of ecological functions.