The study of soil–plant–machine interaction (SPMI) examines the system dynamics at the interface of soil, machine, and plant materials, primarily consisting of soil–machine, soil–plant, and plant–machine interactions. A thorough understanding of the mechanisms and behaviors of SPMI systems is of paramount importance to optimal design and operation of high-performance agricultural machinery. The discrete element method (DEM) is a promising numerical method that can simulate dynamic behaviors of particle systems at micro levels of individual particles and at macro levels of bulk material. This paper presents a comprehensive review of the fundamental studies and applications of DEM in SPMI systems, which is of general interest to machinery systems and computational methods communities. Important concepts of DEM including working principles, calibration methods, and implementation are introduced first to help readers gain a basic understanding of the emerging numerical method. The fundamental aspects of DEM modeling including the study of contact model and model parameters are surveyed. An extensive review of the applications of DEM in tillage, seeding, planting, fertilizing, and harvesting operations is presented. Relevant methodologies used and major findings of the literature review are synthesized to serve as references for similar research. The future scope of coupling DEM with other computational methods and virtual rapid prototyping and their applications in agriculture is narrated. Finally, challenges such as computational efficiency and uncertainty in modeling are highlighted. We conclude that DEM is an effective method for simulating soil and plant dynamics in SPMI systems related to the field of agriculture and food production. However, there are still some aspects that need to be examined in the future.