The present invention relates to the technical field of rice breeding, and provides a method for breeding colored rice two-line hybrid rice. The method comprises: carrying out hybridization by using colored rice C as a male parent and a two-line sterile line S as a female parent, and carrying out backcrossing with the female parent to obtain BCnF2 generation seeds; selecting male sterile plants, performing a paired test cross on the male sterile plants and a two-line restoring line R, and selecting and maintaining homozygous sterile line plants having colored seed coats, as well as corresponding hybrid seeds; detecting seed heterosis, and selecting and maintaining hybrid plants and sterile line plants having heterosis so as to obtain colored rice sterile line seeds; identifying the fertility, yield, quality and resistance of the sterile line to obtain excellent colored rice sterile line plants; and breeding and producing seeds to obtain a colored rice two-line hybrid system.
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