There were three landforms (i.e. desert, bedrock platform and loess gully) in deep-buried coalfield of northern Ordos Basin. Water inflow of working face in desert area was 1~2 orders of magnitude larger than that in other landform areas. In order to find out the key controlling factors of the directly water filled aquifers on the roof of the coal seam, we carried out research from the aspects of topography, landform and geological sedimentation. The results showed that desert landform provides abundant recharge water for underlying aquifers because of gentle topography, large precipitation infiltration coefficient, thick and water-rich quaternary system. While bedrock platform and loess gully landform were the water sources with weak recharge capacity of underlying aquifers. The sandstone-mudstone interbedding structure formed by continental deposits resulted in the absence of regional stable aquifers in Jurassic and Cretaceous strata on the roof of coal seams. Pumping tests of boreholes showed that all strata belong to weak to medium water-rich aquifers. The groundwater level of Cretaceous aquifer decreased by 20~130 m in three mines. There was a close hydraulic relationship between shallow and deep aquifers. The Mesozoic strata belonged to fluvial deposits. Qilizhen sandstone and Zhenwudong sandstone aquifers were mainly developed on the roof of the coal seam, which were characterized by thick medium-coarse sandstone sections. The geological and sedimentary conditions of direct water-filled aquifer were similar, but the amount of borehole water, cumulative pre-drainage water and water inflow from goaf in desert geomorphic area were much larger than those in bedrock platform and loess gully geomorphic area. The water-rich of the aquifer was mainly controlled by geomorphology, and the water sources of the deep aquifers were meteoric precipitation and Quaternary aquifer. In different mines with similar Quaternary conditions in Mu Us Desert, there were also great differences in the amount of borehole water, cumulative pre-drainage water and water inflow from goafs. The difference was related to the thickness and lithology of the aquifers. It reflected that the geological sedimentary conditions of the coal seam roof were also important factors to control the water-rich of the aquifers. Topography, landform and geological sedimentation were the key factors to control the water-rich of the aquifer directly and the water inflow from the working face.