The experiment took Malus robusta Rehd. as rootstock, on which grafting M9, M7, SH38, T337, SH6, SH1, JM7, GM256, ‘Liaozhen 2’, M26, B9. To analyze the correlation among different indexes by determining grafting survival rate, germination rate, plant growth, leaf anatomical data, we studied these 11 dwarf rootstocks by principal component analysis(PCA) and hierarchical cluster analysis(HCA). To learn grafting affinity of different dwarf interstocks with M. robusta Rehd and evaluate their dwarfing traits, we investigated the growth characteristics and leaf anatomical structure of 11 dwarf rootstocks on M. robusta Rehd.. The results showed that: (1) 11 dwarf rootstocks had affinity with M. robusta Rehd, which M26 and SH38 had the strongest affinity. (2) The correlation analysis showed that dwarfing of plant have a negative relatoin with plant height, length of plant internode, diameter ratio, the ratio of upper epidermis thickness, stoma density, thickness of spongy tissue, and its positive with leaf length to width ratio, palisade tissue to spongy tissue ratio, thickness of leaf, thickness of palisade tissue. (3) PCA got four principal components and represented 91.573% of the total variability. The PC1 was related to thickness of leaf, thickness of spongy tissue, thickness of palisade tissue, and the PC2 included length to width ratio, related to plant height, length of plant internode, and the PC3 consisted of palisade tissue to spongy tissue ratio, diameter ratio, and the PC4 was stoma density. (4) According to the result of PCA, 11 dwarf rootstocks were divied ino four types by HCA. The first types includes SH1, SH38, SH6, M7, M26 and the second covers B9, JM7, The third class contains T337, M9, GM256 and the fouth is ‘Liaozhen 2’, which was consistent with the results of PCA. As a result, 11 apple dwarf rootstocks had a better affinity with M. robusta Rehd., which the ranking of dwarf was: ‘Liaozhen 2’ > GM256 > M9 > T337 > JM7 > B9 > M26 > M7 > SH6 > SH38 >SH1.The plant of dwarfing was estimated by plant height, length of plant internode, diameter ratio, the ratio of upper epidermis thickness, stoma density of leaf, thickness of spongy tissue, thickness of palisade tissue, palisade tissue to spongy tissue ratio and thickness of leaf.