Yunnan cherry-tomato and Xinjiang cherry-tomato were very similar in appearance. But they are different in taste and nutritive value. A nondestructive identification method of cherry-tomato variety based on multi-spectral image technology is proposed in this paper. Fifty Yunnan cherry-tomatoes and fifty Xinjiang cherry-tomatoes were selected, and photos were taken by Duncan MS3100 3CCD multi-spectral imager. Threshold based segmentation and mathematical morphology method were used to process the images. Nine characteristic variables were calculated to establish discriminant analysis model (DA) and least square-support vector machine model (LS-SVM). The prediction accuracy of discriminant analysis model was 72.5% and that of LS-SVM model was 80%. The results showed that LS-SVM model could identify Yunnan cherry-tomato and Xinjiang cherry-tomato well.