The invention discloses a computer method for comparing similarity of different plant forms. The plant topological structure features, peripheral contour features and organ geometry structure information are utilized, and the method comprises the steps of firstly adopting the simplified topological structure of a tree graph describing plant, then computing the similarity of the topological structure based on a tree graph editing distance method, then computing the similarity of three-dimensional convex hulls comprising plants among projections of a plurality of planes based on the two-dimensional graph similarity algorithm, on the basis of the similarity, integrating two-dimensional similarity values in all the projections so as to compute the similarity of peripheral contours of the plants, then, comprehensively considering the geometric attribute of subtrees of all levels, computing the similarity of geometric details of the plants, finally, fusing multi-feature information of the plants, and calculating the similarity among different plant structures. According to the method, form similarity of the different plants can be quantized, and the aim of distinguishing varieties or subjects of the different plants through the similarity can be achieved.