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This study aimed to improve runoff simulations and explore deep soil hydrological processes for a watershed in the center of the Loess Plateau (LP), China. This watershed, the Wuding River Basin (WRB), has very complex topography, with soil depths ranging from 0 to 197 m. The hydrological model used for our simulations was the Community Land Model (CLM) version 5 developed by the National Center for Atmospheric Research. Actual soil depths and river channels were incorporated into CLM to realistically represent the physical features of the WRB. Through sensitivity tests, CLM with 150 soil layers produced the most reasonable results and was adopted for this study. Our results showed that CLM with actual soil depths significantly suppressed unrealistic variations of the simulated sub-surface runoff when compared to the default simulations with a fixed soil depth of 8 m. In addition, CLM with higher-resolution soil layering slightly improved runoff simulations, but generated simulations with much smoother vertical water flows that were consistent with the uniform distribution of soil textures in our study watershed. The runoff simulations were further improved by the addition of river channels to CLM, where the seasonal variability of the simulated runoff was reasonably captured. Moreover, the magnitude of the simulated runoff remarkably decreased with increased soil evaporation by lowering the soil water content threshold, which triggers surface resistance. The lowered threshold was consistent with the loess soil, which has a high sand component. Such soils often generate stronger soil evaporation than soils dominated by clay. Finally, with the above changes in CLM, the simulated total runoff matched very closely with observations. When compared with those for the default runoff simulations, the correlation coefficient, root-mean-square error, and Nash Sutcliffe coefficient for the improved simulations changed dramatically from 0.02, 10.37 mm, and -12.34 to 0.62, 1.8 mm, and 0.61. The results in this study provide strong physical insight for further investigation of hydrological processes in complex terrain with deep soils. [ABSTRACT FROM AUTHOR]