The Wadi sheep (WAD) is a unique Chinese indigenous breed previously reported to show adaptation to humid and saline–alkali lowlands, disease resistance, high fecundity, and favorable meat quality. However, the recent widespread introduction of commercial sheep breeds has led to a sharp decline in the purebred WAD population, posing serious threats to the preservation of its unique genetic resources. Therefore, there is an urgent need to assess the current population structure and genetic diversity of WAD to support its conservation and sustainable utilization. In this study, we systematically analyzed genomic variation, population structure, and selection signatures using whole-genome resequencing data from 30 WAD sheep and 80 publicly available genomes representing five other breeds obtained from the NCBI database. Population genomic analyses revealed that WAD retains substantial genetic diversity and exhibits a distinct population structure, shaped by its unique breeding history. Selection signature analyses using F_ST, π ratio, and XP-EHH identified 457 candidate genes under positive selection, which are associated with key biological processes including environmental adaptation, immune defense, muscle traits, growth, and reproduction. These findings identify genomic regions potentially related to reported WAD traits and provide a theoretical basis for its conservation, molecular breeding, and sustainable utilization in lowland environments.