Metropolitan areas are important for engaging in fierce global competition. Cities in metropolitan areas in China are generally characterized by a core-periphery structure. The Yangtze River Delta metropolitan area (YRD) is a national strategic region in which Shanghai, as a central city, drives the economic growth of hinterland cities. Exploring the spatiotemporal characteristics and influencing factors between the central city and its hinterland cities in the YRD can provide a basis for promoting regional development. Based on the headquarters-branches and enterprise investment data from 1978 to 2019, this study analyzes the spatiotemporal characteristics and influencing factors of enterprise linkages between Shanghai and its hinterland cities in the YRD. Our results reveal the following: (1) the headquarters-branch linkages between Shanghai and its hinterland cities manifest polarization characteristics, with different polarized characteristics among the three provinces; (2) the enterprise investment linkages between Shanghai and its hinterland cities are getting closer, but the key cities for investment in each province are different; (3) economic strength is a core factor that affects whether Shanghai establishes enterprise branches in its hinterland cities; and (4) the enterprise investment linkages between Shanghai and its hinterland cities depend on whether a city has a comparative advantage.