Dwarfing rootstocks can improve the plant architecture of apple trees and increase production. Gibberellins (GAs) are crucial for plant growth and dwarfing traits. The receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), plays an important role in the regulation pathway. However, the growth regulatory mechanism of GID1 in dwarf apple rootstock seedlings is not clear. In this study, we selected dwarf apple rootstock ‘SH6’ and its cross parents as materials to clone the GA receptor gene GID1c. There were two different sites in the alpha/beta hydrolase domain. The expression of GID1c in ‘SH6’ was lower than that in Malus domestica cv. Ralls Janet, with the decrease of GA content. We further conducted GA3 treatment and overexpression of GID1c in tissue culture seedlings of ‘SH6’, and the results showed that the expression of GID1c and biosynthesis genes increased and promoted the accumulation of hormone contents, which ultimately regulates the growth of ‘SH6’ dwarf apple rootstock seedlings. Our results suggest that GID1c may affect the plant architecture and dwarf traits of dwarfing rootstock and accelerate its application in orchards.