The purpose of the research is to screen the genes that affect the high fecundity of small-tailed Han sheep, and to provide theoretical basis for breeding improvement and crossbreeding improvement of small-tailed Han sheep. In this study, a total of 21 purebred and pluriparous small-tailed Han sheep with stable pedigree were selected in which 11 sheep (6 in the high-yield lambing group and 5 in the low-yield lambing group) from Jilin and 10 sheep (5 in each of the high-yield lambing group and low-yield lambing group) from Shandong, and blood samples were collected for the whole genome resequencing. The results showed that a total of 3,074 candidate genes shared by the two regions were screened based on the difference in allele frequency, 16 candidate genes shared by the two regions were screened based on the population differentiation index, and 511 candidate genes shared by the two regions were screened based on the nucleotide diversity ratio. Six shared genes were obtained by the intersection of the above three methods, namely CPNE4, CTNNA2, LOC114114249, LOC132659407, MBD5 and SLC6A15, which are expected to be candidate genes affecting high fecundity of small-tailed Han sheep.