The primary method of controlling apple tree size is by using dwarfing rootstocks. While dwarfing rootstocks are the most common practice for controlling size in fruit trees, there are many other methods or techniques used to control the size and vigor of trees. Any practice increasing the harvest index or proportion of biomass going into fruits rather than wood or leaves will tend to reduce the size (total volume or biomass) and vigor (rate of growth) of trees. These horticultural practices can be used to control tree size.
For more information, see this article on Controlling Apple Tree Size by Horticultural Means.
Answer provided by Robert Crassweller, Penn State University