The invention discloses a traceless double-target genome editing system based on CRISPR/Cas9 and lambda-Red. The system is characterized in that 1, pKS9 has the molecular weight of 11,681 kb, is a thermo-sensitive plasmid, and contains cas9 and recX genes induced by tetracycline, lambda-Red integrity alpha-beta-gamma recombinase genes induced by arabinose, and resistance genes ampr; 2, pCSK has the molecular weight of 2,914 kb, and contains two sgRNA insertion sites for specific recognition of genomes, two spacer region gRNA sequences which are induced by rhamnose and used for plasmid elimination and resistance genes kanr; 3, when a homologous arm is 27 bp, the two-point mutation efficiency is both at 92% or above; when the homologous arm is 40 bp, the 1kb replacement efficiency of the twogenes is 60% or above, and when large-fragment gene replacement and point mutation are carried out simultaneously, the respective editing efficiency is not influenced.