The invention discloses a polypeptide pair for specifically recognizing a muscle myostatin gene as well as an encoding gene and an application of the gene. The polypeptide pair provided by the invention comprises a polypeptide I and a polypeptide II; double-chain amino acid in the polypeptide I sequentially comprises 2-3, 36-37, 70-71, 104-105, 138-139, 172-173, 206-207, 240-241, 274-275, 308-309, 342-343, 376-377, 410-411, 444-445, 478-479 and 512-513 of the sequence 3; and double-chain amino acid in the polypeptide II sequentially comprises 2-3, 36-37, 70-71, 104-105, 138-139, 172-173, 206-207, 240-241, 274-275, 308-309, 342-343, 376-377, 410-411, 444-445, 478-479, 512-513 and 546-547 of the sequence 5. The polypeptide pair provided by the invention can specifically recognize the muscle myostatin gene, and has important application value in obtaining high-quality pig breeds with high lean meat percentage by knockout or modification of MSTN on pigs.