Study on the morphological characteristics and genetic mechanism of wheat root system under drought stress is the basis of improving drought tolerance and stabilizing wheat yield. Genome-wide association study (GWAS) was conducted on drought resistance coefficient of wheat root traits at seedling stage, and significant correlation loci and candidate genes were identified to provide information for genetic improvement of wheat drought tolerance. In this experiment, 300 domestic and exotic excellent wheat varieties (lines) were treated by PEG-6000 to simulate drought stress at seedling stage, followed by measurement of wheat root-related phenotypic characters. Genome-wide association analysis of drought resistance coefficients of eight traits including longest root length, total root length, root surface area, root volume, root average diameter, root tip number was performed using a hybrid linear model MLM (Q+K) using 90K SNP, and candidate genes were mined for significant association loci of stable inheritance. The root traits of wheat varieties (lines) showed abundant phenotype variation under drought tolerance, with the variation coefficient of 0.17-0.58, the polymorphic information content (PIC) of 0.01-0.38, and the LD attenuation distance of 7Mb. The population structure analysis suggested three subgroups in this collection. GWAS analysis identified a total of 41 SNPS, which were significantly associated with root drought resistance traits, and mainly found on chromosomes 1B, 2B, 3A, 3B, 5A, 6B and 7B. The phenotype variation explained by a single locus ranged from 3.91% to 8.04%. Thirteen significant association loci were found in two or more traits, distributed on chromosomes 1B, 1D, 2A, 2B, 3B (2), 4A, 4D, 5A, 5B, 6B (2) and 7B, explaining 3.99%-7.05% of the phenotype variation. Tdurum_contig71499_211, Gene-1743_858 and Tdurum_contig28552_211 were significantly associated with 4-5 traits including root fresh weight, root surface area, root dry weight, root volume or root total length and root tip number. Three loci contributed to 4.12%-5.37%, 5.77%-6.70% and 4.10%-5.22% of genetic variation, respectively. Eleven candidate genes were proposed by mining 41 significant association loci of stable inheritance. With gene annotation information, TraesCS3B01G392300 (Calcium-dependent lipid-binding domain-containing protein) is known to be involved in Ca2+ level stimulation response, TraesCS1D01G036900 (Cysteine receptor-kinase protein) and TraesCS5A01G370400 (Serine protein kinase) play important roles in drought, high salt stress and various signaling processes in growth and development. TraesCS7B01G440700 (Cytochrome P450) might function in cell defense against toxic substances. These annotated genes might be used as important genes of drought tolerance in wheat.