The rapid urbanization in the region has caused a shift in land-use structure and, as a result, the degrading of ecosystems. Elucidating the spatial–temporal evolution of ecosystem services (ESs) and ecological function zoning, it was beneficial to develop land use optimization strategy structures for different regions to support regional sustainable development. Taking the Nanjing Metropolitan Area (NMA), China, as a research area, we investigated the spatial–temporal evolution of land use and ESs in 2000, 2005, 2010, 2015, and 2020 by using biophysical models, quantified the trade-offs/ synergies and constraint effects among ESs using Spearman coefficients and constraint lines, and subsequently realized ecological function zoning through the Self-Organizing Feature Map (SOM) and Support Vector Machine (SVM) models on this basis. The results indicated that: (1) constructed land was the greatest area expansion type (an increase of 2,864.46 km2), while cropland was the primary source of its increase (89.69% of the total transfer of constructed land); (2) Habitat Quality (HQ), Landscape Aesthetics (LA), Net Primary Production (NPP), Soil Retention (SR), Nitrogen Retention (NR), and Water Yield (WY) showed a general spatial pattern of “high in the southern mountains and low in the northern plains”, whereas Crop Production (CP) was more susceptible to create trade-offs with other ESs and has four types of constraint effects; (3) to ensure the maximal spatial variation in geography condition, we combined the SOM-SVM to divide the NMA area into 6 ecosystem service zones and advised land development and utilization by zoning characteristics. In addition, we compared the outcomes of zoning before and after SVM optimization to demonstrate the suitability of combining the SOM-SVM approach in zoning. Our research can provide a reference for the sustainable management of regional land resources and landscape planning.