This study selected the Yangtze River Delta urban agglomeration as the research area, combining it with the current situation of the transportation development of the Yangtze River Delta urban agglomeration to construct the urban agglomeration transportation integration index system and evaluate the development status of the Yangtze River Delta urban agglomeration transportation integration. The study examined the influence mechanism of transportation infrastructure on service industry agglomeration. The results are as follows: (1) From 2011–2020, the Yangtze River Delta urban agglomeration’s transportation integration index showed a clear upward trend. (2)The development of transport integration in urban agglomerations has heterogeneous effects on local service agglomeration. The development of the integration level of local transportation has a certain inhibitory effect on the agglomeration of local service industry. The transportation integration of the Yangtze River Delta urban agglomeration plays an important role in promoting the agglomeration of local wholesale and retail industry, transportation, storage and postal services. (3) The transportation integration of urban agglomeration can affect the agglomeration of service industry through the knowledge spillover brought by the free flow of various factors. The knowledge spillover effect caused by local transportation integration can promote the agglomeration of local service industry to a certain extent. The Yangtze River Delta urban agglomeration needs to accelerate the construction of trans-provincial and trans-municipal transportation infrastructure, and further improve the connectivity level of the urban agglomeration, so as to promote the integrated development of high-quality transportation in the Yangtze River Delta urban agglomeration.