Green and high-quality development of China’s territorial space is an inevitable requirement for implementing the new vision and building the new development pattern. The paper builds the evaluation model of urban-agriculture-ecology space to scientifically analyze its spatial function characteristics, and makes spatial function optimization zoning to clear priorities and directions for the development of Yangtze River Delta. The results are as follows: (1) the spatial distribution of urban and agricultural functions has a high overlap, which are mainly concentrated in Shanghai, southern Jiangsu and coastal areas of Zhejiang, but the ecological functions are obviously weak, decreasing from southwest to northeast; (2) according to the improved two-dimensional graph theory clustering algorithm, Yangtze River Delta is divided into six function zones, and our study puts forward scientific countermeasures and suggestions for the rational utilization and development of land space based on the actual characteristics of each functional zone; (3) the zoning factor proposed and the zoning method well maintains the continuity of the functional areas and the integrity of the administrative areas. Hence, it has a good application prospect in the functional optimization, providing the scientific basis and reference value for the spatial planning and integrated development of cross-provincial areas with the goals of high-quality development.