Economic globalisation has accelerated the cross-regional flow of resource elements and broken through the constraints of traditional regional administrative boundaries. Urban agglomerations are core carriers that drive and accelerate regional integration development and can promote the division of urban functions and cooperation. This study considers the Nanjing metropolitan area as a case study to construct a comprehensive first-degree evaluation index system for cities from a factor-flow perspective, focusing on economic, cultural, and transportation connections. We found that (1) Nanjing, which has long been ranked first, shows a downward trending score, dropping from 0.956 in 2017 to 0.937 in 2023; (2) The comprehensive first-degree spatial structure of metropolitan-area cities presents a network hierarchical development feature of “one core, multiple centres, and multiple areas”. With Nanjing as the regional core city, Chuzhou (0.879), Yangzhou (0.915), and Wuhu (0.897) as sub-centre cities, and other cities as sub-regional nodes, the urban system structure gradually forms; (3) The indicators of economic (0.166 **), cultural (0.226 **), and transportation (0.644 ***) element connections were interrelated and mutually reinforced, forming a unified entity with internal connections. This study quantitatively measured the level of integrated development in the Nanjing metropolitan area and provided a reference for formulating regional policies.