Whole-genome resequencing is useful for identifying genetic variations for phenotypic diversity and for revealing the in-depth genomic characteristics associated with adaptation to various ecoregions. Adaptability traits in a diverse range of ecological environments are key to the survival of sheep. Mongolian sheep and its subspecies (Hu sheep and Tan sheep) differ in a number of important traits, especially reproductive traits; however, the potential genetic information still uncertain. In this study we performed pooled whole-genome resequencing of 52 sheep samples (20 Mongolian sheep, 20 Hu sheep and 12 Tan sheep) distributed in different ecoregions to examine the genetic variation. We report genome characterization of three native Chinese domestic sheep breeds discovering 3,537,483 SNPs and 47,890 InDels using whole genome resequencing. The present study emphasizes the genetic diversity, extending our previous study. The genomic regions related to reproductive processes and immune system process of the stress responses according to GO analysis. Altogether, we found reproductive related genes (BMPR1B, BMP15, GDF9 and MTNR1A) and immune related genes (PGLYRP2, TRIM15, TRIM40, SOCS7 and TFAM) in the three sheep breeds. Our results provide a valuable resource of the genomic information for identifying genes associated with important economic traits in sheep and for understanding the genetic characteristics of adaptation to different ecological environments.