Abstract: In this study, the rootstock was Malus micromalus, 5 interstocks were M26, SH1, Y-1, Y-B094 and Y- C002, respectively,‘Fuji Nagafu No.2’grafted on 5 interstocks was taken as material. Anatomical structures of the leaves and branches were compared using permanent paraffin section and optical microscopy. The results showed that there were differences among epidermis thickness, palisade tissue thickness, spongy tissue thickness, palisade tissue/ spongy tissue ratios, and leaf thickness of‘Fuji Nagafu No.2’leaves grafted on 5 different interstocks. There was a positive correlation between palisade tissue thickness and dwarf potentiality, Y- 1, M26 and Y- B094 showed dwarf, SH1 showed semi- dwarf, and Y- C002 tended to be standard. There were also differences among cross-sectional diameter, cortical thickness, phloem thickness, xylem thickness, xylem thickness/ phloem thickness, pith diameter of‘Fuji Nagafu No.2’branches grafted on 5 different interstocks. There was a positive correlation between xylem thickness / phloem thickness ratio and dwarf potentiality, the dwarfing ability of 5 interstocks was in an order as: Y-B094 ＞Y-1 ＞ M26 ＞SH1 ＞ Y- C002, consistent with actual field performance. Different interstocks influenced structures of leaves and branches of aboveground scion, thereby affected their physiological metabolism, and demonstrated standard or dwarf traits.