Urban-rural integration has been found to be an inevitable trend in the development of urban-rural relations and a vital measure to tackle the unbalanced and uncoordinated development between urban and rural areas. Most existing studies on the development of urban-rural integration have only estimated its level and factors and compared the heterogeneity of cities in sample regions. Few studies have focused on the interactions between different categories of urban-rural integration levels. Accordingly, to fill the above research gap, an evaluation index system of the development of urban-rural integration is built in this study from four economic-social-spatial-ecological dimensions, the spatial and temporal evolution characteristics of the development of urban-rural integration in 27 central cities in the Yangtze River Delta region between 2003 and 2020 are analyzed, and the intrinsic dynamic shock effects are empirically investigated using a panel vector autoregression (PVAR) model. This study suggests the following points: (1) the development of urban-rural integration in the Yangtze River Delta region tends to increase while fluctuating and experiences an evolutionary process of “severe dysfunction–moderate dysfunction–mild dysfunction”, with an overall positive development trend. (2) In the study period, the agglomeration effect of the level of the development of urban-rural integration in the Yangtze River Delta has been strengthened continuously, and the overall spatial distribution pattern has changed from “low level, low gap” to “high level, high gap”, showing the characteristics of decreasing class distribution step by step, with Shanghai and Anqing as the markers from east to west. (3) All the endogenous variables of the development of urban-rural integration show a continuous positive response to their own shocks, thus suggesting that the respective variable has a certain path dependence on itself. Shocks of urban-rural ecological integration are capable of boosting the improvement of urban-rural economic integration and urban-rural social integration development, and shocks of urban-rural social integration contribute to the improvement of urban-rural ecological integration. The important policy implication of this study is that an intra-regional linkage and coordination mechanism should be built in the future, while the focus should be placed on the heterogeneity of regional development, and policies and measures regarding development of urban-rural integration in a disaggregated manner should be developed, so as to facilitate the improvement of the level of regional development of urban-rural integration.