This paper proposes a sustainable agricultural development index (SADI) and a hybrid grey model for measuring the changes in agricultural sustainability over time. Firstly, a comprehensive indicator system for co-evaluating the level of agricultural economy, resource, environment, ecology, technology and rural society is presented based on a holistic understanding of agricultural sustainability. Then, the entropy-based TOPSIS model, grey prediction theory and genetic algorithm are combined to build a synthesis method for evaluating and predicting agricultural sustainability and detecting its regional heterogeneity. Furthermore, an empirical study at a provincial scale is conducted by collecting panel data from 2003 to 2017. The result shows that regional agricultural sustainability in China will continue to improve, with different rates in the different provinces from 2020 to 2030. And the regional heterogeneity of agricultural sustainability will increase significantly.