How complex life-history traits evolve under rapid climatic drying is a central question in evolutionary biology. Indigenous sheep maintained under pastoral systems experience strong, spatially structured selection on reproductive timing and thermotolerance, yet the genomic architecture and repeatability of these responses remain unclear. We sampled multiple native sheep populations spanning replicated aridity and heat-load gradients. Animals were phenotyped for puberty onset, litter size, lamb survival, and field thermophysiology (rectal temperature, respiration rate, body condition). Genomes were assayed using high-density SNP genotyping complemented by RNA-seq from peri-pubertal granulosa cells. After modeling structure and relatedness, we combined genotype–environment association tests (LFMM, redundancy analysis) with selection scans (iHS, XP-EHH) and fitted reaction-norm animal models to quantify G×E. Expression QTL colocalization linked variants to gene regulation; GO and network enrichment interpreted pathways. Dozens of climate-associated loci clustered in modules tied to KNDy–GnRH signaling (e.g., KISS1/KISS1R, TAC3), ovarian steroidogenesis (STAR, CYP19A1), and cellular stress responses (heat-shock and vasoregulatory genes). Signals were dominated by soft sweeps and allele-frequency clines repeated across eco-clines, consistent with polygenic and convergent adaptation rather than single large-effect mutations. Reaction-norms revealed significant G×E for reproductive output, and polygenic indices derived from climate-associated SNPs predicted between-population variation in puberty timing and lamb survival under heat. Colocalization with granulosa-cell eQTLs implicated cis-regulatory shifts as a common mechanism. Reproductive timing and heat resilience in indigenous sheep evolve via repeatable, polygenic routes channelled through endocrine and stress-response networks. These results illuminate how selection structures complex traits in heterogeneous environments and provide evolution-informed targets for balanced improvement under warming, drying climates.