Based on the theory of water footprint and the spatial processing method of GIS data, this paper makes a comprehensive analysis on the population density, economic benefit and water resources scarcity of Zhoushan archipelago. The results show that the per capita water footprint of Zhoushan archipelago is 830.82 m3/person, which is smaller than that of Hangzhou and Jiaxing in the same latitude of Zhejiang Province. The average population density of water footprint in Zhoushan archipelago is 12.04 person/10,000 m3, showing a trend of high in north and south and low in central China. The average economic benefit of water footprint is 135.11 yuan/m3; the high value area is distributed in the south of Zhoushan archipelago, Dinghai District and Putuo District, where the economy is more developed, the average degree of water shortage in Zhoushan archipelago is 1.41, water resources are relatively scarce, and the pressure of water resources is greater. In view of this, we should improve the residents' awareness of water saving, reduce the discharge of sewage, and pay attention to the rational distribution of water resources among regions to reduce the pressure of water resources in the core urban areas.