The invention discloses a soybean plant rapid three-dimensional reconstruction method based on phenotype-oriented accurate identification, and the method comprises the steps of enabling a user to useKinect to scan a soybean plant, i.e., a soybean plant, at intervals of a set angle, and obtaining a plurality of frames of point cloud scenes where the soybean plant is placed on an automatic rotatingdisc; after removing a point cloud background through straight-through filtering, calculating a rough registration matrix by using a Rodrigs formula according to a rotation angle provided by a user,performing fine registration by using an ICP algorithm, performing hierarchical clustering on plant point clouds to obtain skeleton points, setting each point to be adjacent to nearest K points for the skeleton points to obtain a plurality of connected components, performing trunk Dijkstra path growth, branch growth point selection and branch communication component Dijkstra path growth on trunk communication components where root nodes are located, and finally performing three-dimensional visualization of a plant skeleton through a pyvista visualization library. According to the invention, the plant point cloud does not need to be processed in advance through software to obtain the parameters, the purchase expenditure of modeling software and the learning and using time cost of the modeling software are saved, and the invention is more efficient.