The output intensity of water resources has become a subject of increasing concern. Based on spatial autocorrelation, the Gini coefficient, the Theil index, and geographically and temporally weighted models, this work studied the spatial correlation and regional differences of the output intensity of agricultural water and the main factors influencing the output intensity of agricultural water from a spatial–temporal perspective in China from 2003 to 2019. The results show that the output intensity of agricultural water showed an upward trend and that the output in the central region was higher than the output in the eastern region, and the eastern region had higher output than the western region. By analyzing the spatial autocorrelation, it was found that the output intensity of agricultural water presented a significant spatial dispersion trend and showed the spatial difference. The overall difference in the output intensity of agricultural water in China showed an increasing trend, but the widening difference showed an alleviating trend; the main reason for this increase in the overall differences is that the intra-group differences in the three regions were increasing, with the largest intra-group differences being observed in the western region followed by the eastern region and the central region. Population scale, water use scale, water use structure, effective irrigation scale, urbanization, and industrial structure create significant spatial differences in the output intensity of agricultural water. However, the level of economic development positively impacts the agricultural water output intensity of all provinces. Therefore, water resource management departments should formulate water resource management policies based on regional water conditions and the differences between influencing factors.