Root system morphology is important for sustainable agriculture, but the genetic basis of root traits and their relationship with shoot traits remain to be elucidated. The aim of the present study was to dissect the genetic basis of root traits at late growth stages and its implications on shoot traits in wheat. Using 323 wheat accessions, we investigated phenotypic differences in root traits at booting and mid-grainfill stages in PVC tubes, and shoot traits including plant height (PH), canopy temperature (CT) and grain yield per plant (YPP) in field experiments, and performed a genome-wide association study with a Wheat 660K SNP Array. Deep-root accessions had lower CT and higher YPP than shallow-root ones, but no significant relationship was identified between root dry weight and shoot traits. Ninety-three significantly associated loci (SAL) were detected by mixed linear model, among which three hub SAL (Co-6A, Co-6B and Co-6D)associated with root depth at both booting and mid-grain fill stages, as well as CT and YPP. Minirhizotron system scanning results suggested that the causal genes in the three SAL may regulate root elongation in the field. The heritable independence between root depth and PH was demonstrated by linkage disequilibrium analysis. The YPP was significantly higher in genotypes which combined favorable marker alleles (FMAs) for root depth and PH, suggesting that deep-root and shorter plant height are suitable traits for pyramiding target alleles by molecular marker assisted breeding. These results uncovered promising genomic regions for functional gene discovery of root traits in the late growth period, enhanced understanding of correlation between root and shoot traits, and will facilitate intensive study on root morphology and breeding through molecular design.