Abstract: Polyploidy, a crucial mechanism of plant evolution has been identified as the most important driving force for species evolution. In order to objectively and scientifically determine chromosome polyploidy, a new recognition method is proposed. In this paper, the whole genome data of Vitis vinifera and Salix sinopurpurea were taken as the research object, combined with genome-wide collinearity and synonymous substitutions rate（Ks）, six measurement features were constructed, which were the total length of homologous segments, Ks threshold for homologous segments, subpoint standard deviation, subpoint maximum gap, subpoint coverage and subpoint rang. According to the significance of each feature in collinearity, after Min-Max normalized values of each feature were fused within and between features to establish gene collinearity evaluation model, and then realized the automatic recognition of chromosome polyploidy. The results showed that with the Vitis vinifera genome as a reference, Salix sinopurpurea experienced a whole-genome duplication, and the related chromosomes with polyploidy signal were provided.The conclusion is consistent with the previous results, which verified the effectiveness of the method. Furthermore, with the Arabidopsis thaliana genome as a reference genome, this method was applied to Brassica rapa and B.oleracea, then obtained the conclusion of whole-genome triplication and related chromosomes with polyploidy signal. The experimental results are also consistent with the relevant literatures, which proved the generalization ability of the method.