The invention relates to an identification method of PPARD major gene, establishment of a molecular breeding method and application in the genetic improvement of breeding pigs. In the invention, by adopting the white Duroc * Erhualian Intercross and the Chinese and exotic breeding pigs of distant population, the whole-genome scan and linkage mapping, the IBD fine mapping of the target region based on a high-density SNP mark and the selection effect analysis of the distant population are carried out, and then the major gene, i.e., PPARD for deciding the traits of pig ears, fat deposition, weight of pig head and carcass traits, and the mutation site of key cause, i.e., G32E are identified. The sites are detected by the modern molecular biotechnology; by adopting the gene-assisted selection method, the beneficial gene-typed individuals are selected for the breeding pigs, thereby the breeding improvement efficiency of the traits of pig ears, fat deposition, weight of pig head and carcass traits are remarkably improved. The invention further discloses an identification course of the gene and the cause mutation site and a method for breeding the traits of pig ears, fat deposition, weight of pig head and carcass traits by using the gene marker of the invention.