The harmonious development of urban rail transit, underground space engineering, and social economy is the key to regional sustainable development. Based on synergetic theory, this paper constructs the coupling coordination evaluation system of “rail transport-social economy” composite system at the scale of a city cluster. With this system, the coupling and coordinated development pattern and characteristics of “rail transit-social economy” in the Yangtze River Delta city cluster from 2002 to 2020 were analyzed. The paper makes a horizontal comparison with the Beijing-Tianjin-Hebei city cluster and the Pearl River Delta city cluster, as well as analyzes the differences in development and existing problems, and puts forward policy suggestions for rail and urban underground space development. The results show that: (1) The rail transit of 11 cities in the Yangtze River Delta shows a “step by step” development pattern. That is “national central city, provincial city, second-tier city, third-tier city, etc.”, accompanied by periodic changes of coupling and coordination degree. In addition, there is also the phenomenon of unbalanced development within the region; (2) From 2002 to 2020, the development of rail transit in the three city clusters shows a situation of “the overall supply is lacking and lags behind the social economy for a long time”. Among them, the Pearl River Delta city cluster has the most serious lags. Multi-channel financing, speeding up the construction of the rail transit scale according to local conditions, and improving operating efficiency are considered to be the keys to solve this problem; (3) In general, the coupling between rail transit and the social economy in the Yangtze River Delta city cluster is better than that in the Beijing-Tianjin-Hebei city cluster and the Pearl River Delta city cluster, but the coordination is at a slight disadvantage.