The water footprint theory provides a new research direction for solving the water shortage problem. Based on the water footprint theory, this paper used the data from Ningxia Statistical Yearbook and Ningxia Water Resources Bulletin to calculate and analyze the blue, green and grey water footprints of the main crops in Guyuan, Ningxia, from 2009 to 2017, with CROPWAT8.0 software. The results showed that the blue water footprint acounted for the highest proportion, the green water footprint came second, and the grey water footprint was the least. It indicated that the water used for crop production in Guyuan City was mainly blue water, and supplemented by green water. Although the gray water footprint is relatively small, it is increasing year by year. It is recommended to adjust the local crop planting patterns according to the specific conditions of water resources, in order to increase the utilization rate of green water, and reduce the use rate of nitrogen fertilizer, and therefore to achieve greater benefits from limited water resources and meet food security and water ecological security needs.