The invention discloses a rice population three-dimensional morphological structure digitalization and visualization reconstruction method, and relates to the technical field of plant three-dimensional digitalization and visualization construction. The method comprises steps: S1, adopting a 'positioning-separation-measurement' method, referring to different coordinate systems, positioning positions and directions of rice plants, stems and blades, and measuring geometrical morphologies of stalks, the blades and other organs; S2, according to different levels, structuring data obtained in S1, and constructing digital rice-population two-dimensional morphological structure; and S3, by utilizing a geometric explanation principle, transforming the positions and directions of the rice plants, the stems and the blades in different reference coordinate systems and the geometrical morphologies of the stalks, the blades and the other organs to the same field coordinate system, and reconstructing digitalization and visualization rice population three-dimensional morphological structure. Through utilization of the method of the invention, the complexity of three-dimensional data acquisition can be effectively reduced, and the visual reconstructed rice population morphological structure and an actual image have a high similar degree.