In the expansive African region, goats display a diverse array of breeds that have evolved over time to adapt to varying local climates and environments. This study involved the analysis of 1591 samples, including 63 domestic breeds and 164 individuals from wild related species, focusing on genetic diversity, population structure, gene flow, selective signals, and landscape genomics. Our findings revealed lower genetic diversity in wild related species, particularly in the mountain goat (Oreamnos americanus). Gene flow was observed between wild Yura goats and North African populations. Introgression analysis identified 34 adaptive genes from wild relatives, particularly those involved in immune response to environmental stress (RGS family). Selection signatures, based on FST, nucleotide diversity (pi), and iHS methods, highlighted genes associated with lipid deposition (GSK3B), energy metabolism (HTR4), and response to cold climates (GLIS1). Landscape genomics further identified 23 climate-related genes, encoding integrin complex (ITGAM/ITGAX), sodium channel (SCN7A/SCN9A), and proton transporter (ATP6V0D1), which regulate cell adhesion, ion homeostasis, and pH balance to cope with pathogen pressure in sub-Saharan Africa, osmotic imbalance in arid environments, and heat stress in the East African plateau. This study provides the first systematic explanation of the multi-directional adaptation mechanisms of African goats to high temperature, drought, and pathogen infection. The adaptive gene modules, such as the ABCG1-AGTR1 metabolic axis, provide precise molecular targets for drought stress of livestock in arid regions, and provide a new paradigm for understanding the evolutionary logic of mammalian environmental adaptation.