As the critical information to study flow transport in soil–plant systems, root distributions and root-water-uptake (RWU) patterns have been studied extensively. However, most root distribution data in the past were collected under surface irrigation. Less research has been conducted to characterize root distributions under sub-irrigation. The objectives of this study were to (1) test if the generalized function of normalized root length density (NRLD) in the literature was applicable to root distributions of winter wheat under natural sub-irrigation, which provides water from subsurface by capillary rise from the water table, and (2) estimate RWU distributions of winter wheat under natural sub-irrigation. Column experiments were conducted to study the distributions of root length density (RLD) and RWU of winter wheat (Triticum aestivum L. cv. Nongda 189) during a growing period of 57 days from planting to tillering stages under surface irrigation and natural sub-irrigation. Data of root distributions and soil water content were collected in the experiments with different treatments of irrigation levels. Results showed that the RLD distributions of winter wheat under both surface irrigation and natural sub-irrigation were of similar patterns. The NRLD distributions under sub-irrigation were adequately characterized by the generalized function. An inverse method was employed to estimate the average RWU rate distributions of winter wheat. In addition, based on the potential RWU coefficient and the NRLD function, a simple approach was developed to predict RWU rates at different depths. The predicted RWU rates had a good agreement with the estimated RWU rate distributions using the inverse method.