Accurate predictions of the mechanical response of root-soil systems are required for assessing and reducing the risk of landslides, surface erosions, and lodging. The present paper proposes the use of the node-to-segment (NTS) approach with the finite element method for predicting contact phenomena between roots and soils, such as collision, sliding, and separation. To obtain reliable predictions for the deformation of such geometrically complex problems, a stabilizing algorithm within the NTS approach is proposed and implemented here. The proposed algorithm prevents the well-known non-uniqueness problem of the pairing algorithm in the NTS approach, which has been an obstacle to applying the approach to root-soil systems. The current method is employed for two numerical examples. The first is an example of validation, in which pullout experiments are re-analyzed to examine the applicability of the method to a geometrically simple root-soil contact problem. It is shown that the current method provides a reasonable prediction of the pullout response, and that both the friction and the cohesion can also be accurately estimated with it. The second is an example of a realistic problem, in which a 2-D lodging experiment, analogous to pile-loading problems, is conducted and simulated to demonstrate the accuracy and applicability of the NTS approach in plant-scale problems with complex root geometries. The relationship between the displacement and the reaction force of the simulation is consistent with that of the experiment, and it enables the visualization of the stress contour and deformation of the rhizosphere.