In order to clarify the correlation between short-shoot Fuji apple tree structure and different factors under different trimming and pruning modes, we investigate the trunk taperingness of free-spindle short-shoot Fuji and slender-spindle short-shoot Fuji, respectively, as well as the total thickness, average thickness, total length and average length of small main branches in the standard demonstration apple garden in Xingtang County of Hebei Province. By SPSS analysis, we study the correlation between trunk taperingness of trees with different shapes and the growth indices of their small main branches. The results show that the trunk taperingness of free-spindle short-shoot Fuji apple is negatively correlated with the total thickness, average thickness, total length and average length of small main branches, but the correlation is not significant; the trunk taperingness of slender-spindle short-shoot Fuji apple is negatively correlated with the total thickness but positively correlated with other factors, and the correlation with average length reaches a significant level. The results of this study can provide a scientific basis for guiding the high-density dwarf rootstock short-shoot Fuji apple tree trimming technology.