Abstract: The disclosure provides a method for breeding Carassius auratus strains without intermuscular bones, which comprises designing knockout target sites for the two copies of the bmp6, bmp6a and bmp6b, in the Carassius auratus genome, and then obtaining F2 generation individuals from a homozygous line with bmp6a and bmp6b double gene mutation through two rounds of gene knockout and screening, and then propagating by using the F2 generation individuals from the homozygous line with bmp6a and bmp6b double gene mutation to form a new Carassius auratus strain with intermuscular bone-deficient. Strains of Carassius auratus with less than 20 intermuscular bones and without intermuscular bones are obtained by the method of the present disclosure.