With the rapid development of the cities, the structure of rivers and lakes in China has gradually evolved toward a singular trend, which has created a series of environmental problems. This paper takes Haikou City as the research area to establish a quantitative analysis index system for the influence of urbanization on water system connectivity. Through ENVI, ArcGIS software and data collection, the data of connectivity patterns and functional indicators of Haikou City from 2000 to 2016 are obtained. The statistical analysis were used to study the relationship between the water system connectivity function index and the water system connectivity morphological index, and to determine the water system connectivity index threshold by combining with the future water function of the Haikou city water system. The results showed that the index threshold is the node connection rate:［1.0152, 1.2471］; the water system ring degree:［0.0049, 0.0111］; the river network density:［0.0585, 0.1786］; the water system connectivity:［0.3384, 0.3541］. The determination of threshold can provide reference for urbanization of water resources planning and management in areas affected by water system, as well as urban construction.