The overexploitation of groundwater in China has raised concern as it has caused a series of environmental and ecological problems. However, far too little attention has been paid to the relationship between groundwater use and the spatial distribution of water users, especially that of manufacturing factories. This study proposed a factory scatter index (FSI) that incorporates the latitude and longitude of each plant and calculates the distance between factories to characterize the degree to which manufacturing plants are scattered in China. It is found that counties and border areas between neighboring provinces registered the highest FSI increase. It seems that the degree of scattering of manufacturing plants is closely related to land planning and management of local governments. Further non-spatial and spatial regression models using 205 provincial-level secondary river basins in China from 2016 show that the scattered distribution of manufacturing plants played a key role in groundwater withdrawal in China, especially in fragile ecological-environment areas. The scattered distribution of manufacturing plants raises the cost of tap water transmission, makes monitoring and supervision more difficult, and increases the possibility of surface water pollution, thereby intensifying groundwater withdrawal. A reasonable spatial adjustment of manufacturing industry through planning and management can reduce groundwater withdrawal and realize the protection of groundwater. Our study may provide a basis for water-demand management through spatial adjustment in areas with high water scarcity and fragile ecological environment.