Ecological security is one of the fundamental guarantees for regional social and economic sustainable development; however, ecological environmental vulnerability threatens regional ecological security, which is essential for evaluating ecological environmental vulnerability in urban agglomeration in the Fujian Delta region. We selected 13 factors, including elevation, slope, lithology, soil type, normalized difference vegetation index, annual mean precipitation, annual mean temperature, population density, per capita GDP, road density, landscape diversity index, degree of land use, and industrial solid waste emissions in 2000 and 2015, based on the spatial principal component analysis method, combined with global Moran 'I and LISA clusters based on five quantitative characteristics, spatial patterns, spatial clustering, vulnerability differentiation of land use, and driving force to analyze the ecological environmental vulnerability and its driving force in urban agglomeration in the Fujian Delta region. The results showed medium ecological environmental vulnerability in urban agglomerations in the Fujian Delta region, but showing an increasing trend from medium to strong vulnerability from 2000 to 2015. From 2000 to 2015, ecological environmental vulnerability showed an overall gradual increasing trend from the southeastern coast to the northwestern inland, with obvious zonal characteristics. The increase in the ecological environmental vulnerability was not obvious in the southeastern coastal area, and even declined in some areas, but increased significantly in the northwestern inland. Ecological environmental vulnerability had a significant spatial autocorrelation, and significant positive correlation, with a significant high-high clustering in the northwestern inland and a significant low-low clustering in the southeastern coastal area. The clustering characteristics showed some spatial migration and expansion over 16 years; from 2000 to 2015, there was a relative heterogeneity under different land use types, and the ecological environmental vulnerability index was always in the following order: forest land > unused land > grassland > farmland > wetland > construction land, with a transition from medium to strong vulnerability. The driving force of ecological environmental vulnerability changed from 2000 to 2015, but population density, landscape diversity, lithology, and soil type were the main driving forces in urban agglomeration in the Fujian Delta region.