Deep soil moisture is fundamental to hydrological cycle and ecosystem sustainability in arid and semi-arid regions. This study examined the combined effects of topographic domain and land use on the spatial variability of deep soil moisture (0–5 m) on the semi-arid Loess Plateau of China. Our results showed that deep soil moisture was generally temporally stable due to the thick loess soil in the plateau region. The depth-averaged soil moisture was slightly lower in the gully domain compared to the hillslope domain but was dependent on the soil depths. Soil moisture variability was clearly larger in the gully domain when compared with that in the hillslope domain in the 0–5 m profile. The mean soil moisture contents in comparable soil depths were lower in forestland than in grassland (and farmland), particularly in the hillslope domain. Land uses had similar vertical distribution characteristics of deep soil moisture for each topographic domain. Soil moisture showed highly significant positive correlations with slope aspect in the hillslope domain and with profile curvature in the gully domain.