To quantitatively analyze the variation of river network structure and water system connectivity caused by urbanization, the river network density, water surface rate, river network complexity, river network structural stability, river network connectivity, and hydrological connectivity of the Qinhuai River Basin in 1990, 2000, 2010 and 2015 were calculated. The evolution process of the water system structure and connectivity in the Qinhuai River Basin were obtained. The statistical method is used to obtain the relationship between the water system structure index and the water system connectivity. The results show that the river network density and water surface rate in the Qinhuai River Basin have been decreasing continuously in the past 25 years. The river channel is characterized by main trunking. The overall scale of the river network in the basin is shrinking. The water system connectivity variation is consistent with the overall trend of river network structure variation, both showing a decreasing tendency. The change is significantly correlated with the water surface rate, river network density and river network complexity.