The lack of a suitable rootstock to control scion growth has limited the development of high-density plantations in pear production, which is partly attributed to poor understanding of the dwarfing mechanism. In the present study, the rootstock of the dwarf-type pear (Pyrus betulaefolia) ‘PY-9’ was identified and used as the material for anatomical analysis. ‘PY-9’ grew to half the tree height of the normal cultivar ‘Zhengdu’, along with fewer internodes and shorter length. Significant differences in growth rate between ‘PY-9’ and ‘Zhengdu’ were detected at approximately 30 days after full bloom, which corresponded with the time of the greatest difference in water potential between the dwarf and normal cultivar. ‘PY-9’ showed a higher photosynthetic rate than ‘Zhengdu’. Anatomical analysis showed that ‘PY-9’ had higher area ratios of both phloem and xylem and more developed vascular tissues than ‘Zhengdu’. The three-dimensional reconstructed skeleton of the xylem from X-ray computed tomography scanning revealed greater intervessel connectivity in ‘Zhengdu’ than in ‘PY-9’, which could contribute to the more vigorous growth of ‘Zhengdu’. This study thus provides the first comparison of the microstructural properties of xylem elements between a dwarfing-type and vigorous-type pear rootstock, providing new insights into the dwarfing mechanism in pear and facilitating breeding of dwarf pear rootstocks to increase crop productivity.