The invention relates to an apple dwarfing self-rooted rootstock SH38 or SH40 large-scale breeding method. The method is suitable for cultivating SH38 or SH40, and specifically comprises the steps oftaking an SH38 or SH40 grafted seedling which is grafted close to the root part and taking malus robusta as a rootstock or a self-rooted seedling as a seed tree, carrying out annual growth branch budnotching, horizontal branch pressing, fixing and soil burying, performing twisting on the new shoot base newly grown from the horizontally pressed branch, carrying out hormone treatment, matrix land-filling, humidity and fertilization management, seedling lifting, and seedling separation to obtain SH38 or SH40 dwarfing self-rooted rootstock. According to the breeding method, the SH38 or SH40 current year-growth semi-lignified shoot does not leave from the parent body to root, and has the advantages that the propagation conditions are mild, the production process is simple, the technical operability and achievability are high, the seedling rate is high, the seedling quality is good, and the like. By adoption of the method of the invention, the apple dwarfing self-rooted rootstock SH38, SH40can realize large-scale and low-cost propagation, thereby obtaining the apple dwarfing self-rooted rootstock SH38 or SH40 with stable traits, neat and consistent tree growth, early flowering and early fruit, fertilizer saving, water saving, land saving and high uniformity of the fruit shape index.