Litter size (total number born) trait has a great impact on the economic success of pork production. The total number born consists of the number of piglets born alive and dead. To clarify the genetic background of litter size, genome-wide association studies were undertaken in the present study. Samples of DNA were collected and genotyped using the Porcine 50K BeadChip from 723 Dongliao Black sows. Using three different models (BLINK, FarmCPU, and MLM), a total of 155 significant SNPs were discovered, six of which had been reported in previous pig reproduction association studies. We suggest that rs81318434, located in the GLI3 gene, might be the promising candidate affecting litter size trait. Our findings may provide insights for uncovering the genetic mechanisms for the litter size of pigs.