Thyroid hormone responsive spot 14 (THRSP) is a nucleoprotein induced by thyroid hormone, which makes an essential effect on the regulation of animal lipogenesis. In order to clarify the genetic mechanisms of the differences between Chinese native pig breeds (fat-type group, FTG) and introduced pig species (lean-type group, LTG) in carcass fat deposition, DNA samples of ear tissues were extracted from FTG(n = 228) composed of Wannan Spotted, Jixi Black and Dingyuan and LTG (n = 92) from Landrace, Large White, Duroc and their hybrid pigs and then detected the SNPs in the coding region of THRSP gene. The effects of SNPs on mRNA folding and protein secondary structure in FTPG and LTPG were predicted using Vienna RNA folding software and YASPIN web services, and their distribution and association with lipogenesis capability in FTG and LTG were analyzed. The results showed that the homologies of nucleotide sequence in coding region of pig THRSP gene with human and cattle were 86% and 88%, respectively. Two SNP sites, G123A and A308G, were located at 123 bp and 308 bp away from the start of the CDS, respectively. The mutation at G123A site was a synonymous mutation, but the mutation at A308G site caused the change of amino acids from lysine to arginine at 103rd site of THRSP protein which resulted in the changes of casein kinase Ⅱ phosphorylation site from TKEE to TREE, mRNA folding and protein secondary structure. The frequencies of alleles 123G and 308A were 0.975 9 and 0.589 9 in FTG, repectively, while that of alleles 123G and 308A were 0.657 7 and 0.815 2 in LTG. The total frequency of gamete 123G308A and 123G308G in FTG achieved 0.975 9, while that of gamete 123A308A and 123G308A in LTG was 0.815 3. Data from the present study imply the association of polymorphism at G123A and A308G sites with lipogenesis capability of pigs and their important regulating role in the expression of lipogenesis genes in pigs.