The ecological conservation and high-quality development of the Yellow River Basin (YRB) has been declared as a major national strategy of China. Surface water availability (precipitation minus evapotranspiration, PME) poses challenges to the sustainability of ecosystems of the YRB. Noteworthy is that the Mongolian section of the YRB (IMYRB) is a critical ecological barrier in Northern China. Soil moisture (SM) changes are highly sensitive to PME and important for regional ecological security. However, SM vs. PME interactions and relevant mechanisms within the IMYRB are poorly understood. We found significant decreases in SM and PME over the east IMYRB (r = 0.7, p < 0.05). During the wet (July, August, and September) and dry (April, May, and June) seasons, as well as the whole year, decreased SM drives increased PME through land-atmosphere interactions over more than 90% of the IMYRB. Reduction in SM decreased evapotranspiration over more than 80% of the IMYRB, increased surface temperature across more than 79% of the IMYRB, boosted atmospheric vertical ascent over more than 75% of the IMYRB, and enhanced moisture convergence and PME. This study highlights the land-atmosphere interactions over the IMYRB, implicating basin-scale impacts of climatic changes on water resources.