A critical challenge in the design optimization of subsoiling and deep-fertilization implements for root pruning during the regreening stage of winter wheat lies in the lack of a validated root–soil discrete element (DEM) model. This study analyzed and measured the geometric morphology of winter wheat root systems in soil during the regreening stage and constructed corresponding geometric models. Based on the DEM framework, a Hertz–Mindlin with bonding model (HMBM) for the wheat root system was developed. The parameters of this model were calibrated using Plackett–Burman (PB) and Box–Behnken design (BBD) methods. Soil particles were simplified to spherical shapes according to particle size distribution analysis, and a discrete element model of soil particles using the Johnson–Kendall–Roberts (JKR) contact model was established. Soil model parameters at three different moisture contents were calibrated with the angle of repose (AOR) as the target response. The accuracy of the root bonding model and parameters, as well as the root–soil contact model and parameters, was verified through pull-out tests and corresponding DEM simulations of single roots in soil. Comparison between experimental and simulated pull-out results confirmed the validity of the developed root–soil DEM model for winter wheat during the regreening stage. This study provides a solid theoretical and experimental basis for future research on root cutting and tillage operations in winter wheat.