<p>Computational Fluid Dynamics (CFD) is a modern numerical analysis technology based on computer numerical simulation models for simulating and analyzing fluid flow, heat and mass transfer, and related physical phenomena. It predicts intricate fluid flow patterns by numerically discretizing and solving the governing equations for describing the conservation mechanics of mass, momentum, and energy in fluid. CFD is instrumental in elucidating the mechanisms underlying complex fluid dynamics and material transport within agricultural settings. This paper systematically reviews the latest research progress of CFD in the design and engineering applications of agricultural machinery. It elaborates on the technical principles, governing equations, and typical computational models of CFD, following by the traditional simulation workflow. The review highlights the practical applications of CFD and the integrated CFD-DEM approach in critical agricultural operations of seeding, conveying, cleaning, spraying, fertilizing, harvesting, drying, and greenhouse climate management. The effectiveness has also been examined in enhancing equipment design, boosting operational efficiency, and minimizing energy use and crop damage. In addition, CFD’s role is summarized for advancing agricultural machinery towards greater efficiency, precision, and intelligence. It critically addresses the existing challenges, for examples the intricacies of multi-physics coupling, scarcity of validation data, and constraints on computational resources. The future development trends are prospected by combining CFD with artificial intelligence and high-performance computing (HPC), aiming to provide a systematic theoretical reference and technical path for digital design and innovation in agricultural engineering.</p>