Plant roots are critical for water and nutrient acquisition, crop growth and development as well as yield formation. Exploring SNP loci significantly associated with root traits in wheat at seedling stage and mining candidate genes, will lay a foundation for understanding the genetic mechanism of wheat root system architecture and breeding wheat elite varieties with better root architecture. In this study, 189 diverse wheat lines were assembled as an association-mapping panel, which were genotyped with Wheat 660K SNP array. Five root traits including total root length (TRL), total root area (TRA), total root volume (TRV), average root diameter (ARD) and root dry weight (RDW) were investigated by growing in hoagland nutrient solution and pure water, and genome-wide association studies were performed. The root traits varied most among these lines under hoagland nutrient solution, while root elongation under pure water was faster than that under hoagland nutrient solution. According to genome-wide association studies, a total of 90 SNPs associating with root traits significantly were identified, using Blink, CMLM, FarmCPU and MLM models in two environments (P≤10-4). Among them, 17 SNPs were detected in both environments and distributed on chromosomes 7A, 1B, 2B, 3B, 7B, 1D, 2D, and 3D, which explained 8.68%-14.07% of phenotypic variation. In addition, 12 candidate genes possibly related to root development were found by mining genes within the interval of significant SNPs with stable inheritance. TraesCS7A02G160600, encoding 3-oxoacyl-[acyl-carrier-protein] synthase, is involved in the synthesis of root fatty acids; TraesCS1B02G401800, encoding syntaxin, plays an important role in plant tropism; TraesCS7B02G417900, encoding aldehyde oxidase, is involved in the synthesis of abscisic acid and regulation of crop root development. Based on genome-wide association studies, 17 significant SNP loci linked with root traits were detected simultaneously in two environments, and 12 candidate genes related to root traits were finally screened out, providing reference for understanding the regulation of root development and molecular marker-assisted breeding in wheat improvement.