Excessive adipose tissue accumulation in sheep disrupts insulin signaling, inducing insulin resistance, and alters energy partitioning mechanisms. These changes adversely affect both ovine health and production efficiency. This study employed whole-genome resequencing to conduct selection signal analysis in long-fat-tailed (Lanzhou fat-tailed sheep) and short-fat-tailed (Hu sheep) breeds, investigating the genetic basis underlying divergent lipid metabolism-related traits between these distinct tail phenotypes. Fifteen healthy adult individuals, each from long-fat-tailed (Lanzhou Large-tailed sheep) and short-fat-tailed (Hu sheep) breeds, underwent whole-genome resequencing. Whole-genome resequencing analyses via F_ST, XP-CLR, and XP-EHH identified 75 significantly selected regions (p < 0.01), revealing eight key candidate genes (DAB1, DPP10, EPHA6, GPC5, KLF12, PAK7, PTPN3, TENM3). Subsequent functional enrichment analysis demonstrated significant enrichment of DAB1 and GPC5 in lipid metabolic processes (GO:0006629). Employing whole-genome resequencing-based selection signal analysis in long-fat-tailed (Lanzhou Large-tailed sheep) and short-fat-tailed (Hu sheep) breeds, this study identified two key lipid metabolism-associated genes (DAB1 and GPC5). These findings provide critical insights for conserving genetic resources and informing molecular breeding strategies targeting divergent tail phenotypes.