Affected by human activities, the naturally occurring river network in the southeastern plain of Yinzhou has gradually evolved into a natural-artificial composite water system, and changes in river connectivity due to changes in river network systems have caused water security problems, including urban flooding. To clarify the river connectivity change and its relationship with the urbanization process, this paper discusses an evaluation method for river connectivity based on complex networks and cellular automata (CA) from the perspective of complex systems, quantitatively analyzes the spatial-temporal characteristics of the structural and functional river connectivity in the study area during the 1990s-2020s, and reveals the impact of river nodes and chains on the connectivity level under the disturbance of natural or human factors. The results contained the following revelations: ① River connectivity showed a decreasing trend in the initial and rapid development stages of urbanization from the 1990s to the 2010s and a limited increasing trend in the optimization and upgrading stages from the 2010s to the 2020s. ② River network degradation and ongoing connectivity decline are found in the northeastern part of the study area. The highest river connectivity exists in Dongqianhukaifaqu. ③ The number of river nodes and chains should be maintained at approximately 80% for normal river connectivity. The nodes of high degree in the inflow area are listed in the key protection areas. ④ Changes in river connectivity are significantly correlated with the urbanization process. Changes in the functional connectivity level affect the magnitude of a flood. This study provides a theoretical basis for river network connectivity improvement and flood prevention in plain areas.