Shenzhen City, which is the first to face industrial transformation and spatial constraint, is taken as an example. By using the industry, space and transportation as the main line, the port-city relationship in the transition is judged from maturity to stagnation, and it has three contradictions: weakened industrial interaction, spatial layout conflict and coastline and land competition. The development of the port-city relationship is proposed to change from focusing on the quantity to on the quality. The coordination strategies of functional upgrading, spatial optimization and improved facilities are put forward: (1)The function of the port should extend to high-value-added industrial chains such as shipping, trade, finance and service industries and increase the connection with the urban industry. (2)The layout of the port gradually should shift from the eastern port area to the western one so as to promote the coordination of the spatial coordination between the western port area and the Qianhai Center. (3)The water-to-water transfer, sea-rail transport should be vigorously developed, and a layout model of “peripheral transfer and multi-layer compound” should be planned to resolve the dilemma of large land gaps in the rear of port.