The invention relates to a pig genome molecular marker excavation method based on combination of LINE1 transposon and a microsatellite primer. The method uses a 5'-terminal nucleotide sequence or a 3'-terminal nucleotide sequence of LINE1 to design a specific primer; according to bioinformatic analysis, the microsatellite sequences widely distributed in the pig genome are obtained to design the microsatellite primer; two primers are combined, and the different types of the pig genomes can be taken as a template for amplification; an amplification strip having clearness, high polymorphism and good repeatability is screened, and clone sequencing is carried out; a sequencing result is subjected to comparative analysis, combination of a side specific primer and a retrotransposon LINE1 specificprimer can be designed, a to-be-verified molecule-labeled primer is used for PCR amplification of different types of individual genome samples, the primer combination capable of clearly amplifying the strip and having polymorphism can be selected, and the molecular marker can be obtained. The method can provides the useful molecular marker for marker auxiliary selection in pig lines identification and breeding.