Drought is one of the most critical abiotic stress factors affecting wheat yield.To identify the key drought-resistant loci and candidate genes in wheat-Thinopyrum intermedium introgression lines, 180 wheat-Thinopyrum intermedium introgression lines were used as materials in the study. Based on the previous drought tolerance identification at the germination stage, 15 drought tolerance related traits were taken as phenotypes combined with genotyping using wheat 55K SNP array, a mixed linear model(PCA+K) was employed for genome-wide association analysis to detect SNPs significantly associated with drought tolerance traits. Candidate gene prediction and haplotype analysis were further conducted for significant loci.The results showed that all the 15 drought-related traits exhibited extensive phenotypic variation, with coefficients of variation ranging from 4.22%-28.53%. Correlation analysis revealed significant or highly significant correlations among the 15 drought-related traits, and the frequency distribution of each trait followed a normal or skewed normal distribution. A total of 69 SNPs significantly associated with drought tolerance traits were detected by genome-wide association analysis with the threshold P≤0.001. Among these, 36 important SNP loci or segments were identified, including cluster-distributed loci, pleiotropic loci, and major-effect loci, which were distributed arcoss 17 chromosomes such as 1A, 1B, 2Aand 2B, explaining 6.20%-12.00% of the phenotypic variation. Comparative analysis indicated that 11 of these were previously unreported drought-resistant loci. A total of 125 candidate genes related to wheat drought tolerance were identified, encoding LEA proteins, rapid alkalinization factor 1, basic leucine zipper (bZIP) transcription factors, calcium-binding proteins, zinc-transporting ATPases, lysine 63-specific deubiquitinase BRCC3, and leucine-rich repeat receptor-like protein kinases and other related proteins. Haplotype analysis revealed significant differences in drought tolerance phenotypes among different haplotypes of the 21 candidate genes, indicating that these genes could be important candidate genes for drought tolerance.