The embodiment of the invention provides a crop plant phenotype analysis method and device, and belongs to the technical field of agricultural informatization. The method comprises the following steps of acquiring the plant morphological data of crop plants; inputting the plant morphological data into a crop plant morphological model, and outputting the stalk morphological data and the missing leaf morphological data of the crop plant. Due to the fact that the stem morphological data and the missing leaf morphological data of the crop plants can be directly obtained through the crop plant morphological model on the scale of the single plant, compared with a three-dimensional reconstruction mode, the workload is smaller, the efficiency is higher, and the high-throughput phenotypic analysis can be conveniently achieved. In addition, only the external leaves of the wheat plant three-dimensional model constructed by the three-dimensional reconstruction methods, such as multi-view imaging. three-dimensional laser radar, etc., has the relatively higher resolution ratio, the point cloud noise of stalks and leaves close to the center of a plant is high, and the accurate three-dimensional reconstruction is difficult to achieve, but the accurate three-dimensional reconstruction and phenotypic analysis can be achieved through the embodiment of the invention.