AbstractPrecision agriculture benefits from point set registration, which can monitor plant health and growth in real time, promote the precise application of fertilizers and pesticides, and provide technical support for achieving sustainable development of agriculture. In this work, we propose a robust point set registration method for precision agriculture based on L*a*b* color guidance, bidirectional search and Cauchy distribution. First, the L*a*b* color guidance is applied to establish accurate correspondences between agricultural RGB‐D data. Second, the bidirectional nearest neighbor search strategy between point sets improves the reliability of establishing correspondences and broadens the convergence domain of the algorithm. Third, Cauchy distribution is utilized as an energy function for noise suppression, which further improves the robustness of the algorithm in dealing with complex vegetation scenes. Finally, results of ablation and simulation experiments indicate that the proposed registration algorithm can achieve more accurate and robust alignment results than other classic and state‐of‐the‐art point cloud registration algorithms to achieve monitoring and comparison of plant growth.