GSK-3 plays an important role on numerous cellular processes involved in the regulation of embryonic development, protein synthesis, glycogen metabolism, inflammatory, mitosis and apoptosis. In this study, we obtained the cDNA and promoter sequences of the porcine GSK-3α gene, analyzed its genomic organization and mapped it to SSC6q12 through comparative mapping method. Moreover, the qRT-PCR analysis revealed that porcine GSK-3α gene was widely expressed in many tissues, and a high expression level was observed in the brain and spleen. In addition, seven single-nucleotide polymorphisms were detected in the promoter region of porcine GSK-3α gene. Association analysis revealed that the GSK-3α Hin1I and MspI polymorphisms both had significant associations (p < 0.05) with loin muscle area, average backfat thickness, thorax-waist fat thickness, and buttock fat thickness. These results provide useful information for further investigation on the function of porcine GSK-3α gene.