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 resistance related indicators 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 indicators. Candidate gene prediction and haplotype analysis were further conducted for significant loci. The results showed that all the 15 drought resistance related indicators exhibited extensive phenotypic variation， with coefficients of variation ranging from 4.22%-28.53%. Correlation analysis revealed that most of the 15 drought resistance related indicators exhibited significant or highly significant correlations， and the frequency distribution followed a normal or skewed normal distribution. A total of 69 SNPs significantly associated with drought tolerance indicators 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 across 17 chromosomes such as 1A， 1B， 2A and 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 late embryogenesis abundant protein， lysine 63-specific deubiquitinase BRCC 36， basic leucine zipper transcription factors， rapid alkalinization factor 1， calcium-binding protein 39， zinc-transporting ATPases， 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.