Platelet-derived growth factor (PDGF) family, exert plays a key role in embryonic development, cell proliferation, cell migration, angiogenesis and reproduction. Related studies about GWAS analyses have found that PDGFD significantly affected deposition of tail fat in sheep, but there are no studies on reproduction in animals. In this study, three breed of sheep were used to find insertion/deletion (indel) fragment polymorphism of PDGFD which including Australian white (AUW) sheep (Meat type, n = 932), Guiqian semi-fine wool (GSFW) sheep (wool type, n = 60) and East Friensian milk (EFM) sheep (dairy type, n = 60). Only a 18-bp variation was polymorphic in the study AUW sheep population and the genotypes of different sheep breed are also specific. Moreover, the association analysis indicated that this variant was associated with litter size of AUW sheep in the first parity (p < 0.05). The litter size of II genotype was significantly lower than other genotypes in the first parity (p < 0.05). We also revealed that the PDGFD gene was relatively conservative in eight species, PDGFD mRNA expression in 832 sheep samples implying this gene was related to reproduction traits. Hence, these finding demonstrated the one-cause multipotency of PDGFD gene. Collectively, these results suggest that this indel can be used as an effective marker for sheep breeding.