The invention discloses a method for stitching fruit tree crown layer organ images. The method comprises the following steps that A, series intensity images of crown layer organs of fruit trees in different growing periods are shot through a PMD camera and meanwhile, series color images of the crown layer organs of the fruit trees are obtained through a color camera; B, adjacent images of the intensity images and the color images are registered respectively; C, overlapping zones of the adjacent images of the intensity images and the color images are fused; D, a stitching effect image of the intensity images and a stitching effect image of the color images are obtained respectively through stitching; E, production of the fruit trees is instructed according to the stitching effect image of the intensity images and the stitching effect image of the color images. The method is suitable for image stitching of the crown layer organs in a year growing period of the fruit trees, the robustness, the instantaneity and the stitching accuracy of the algorithm can satisfy the requirement for three-dimensional reconstruction operation of a crown layer, and the method has a great significance in the improvement in an information level of fruit ranch management such as pruning, flower thinning, production predication and picking.