In order to explore genetic loci that associated with arabinoxylan and fructan content in common wheat (Triticum aestivum L.), a genome-wide association study (GWAS) was conducted using the wheat 660K genotyping assay in a diverse panel of 243 wheat genotypes. Field trials for arabinoxylan and fructan content were conducted in two locations for two years. The results indicated that most cultivars evaluated showed arabinoxylan content of 0.288%-0.869%, and fructan content of 0.81%-2.14%. A total of 671 significant SNPs were detected for arabinoxylan content, each of which contributed the phenotypic variation from 10.6% to 19.6%. In those SNPs, nine SNPs were detected in two environments, of which 1, 3, 1, 1 and 3 were distributed on chromosomes 5A (35.64 Mb), 5B (665.56-671.09 Mb), 5D (220.51 Mb), 6A (614.81 Mb), and 7A (693.57-693.76 Mb). The significant SNPs on 5B were located in a 5.53 Mb region containing 62 annotated genes, and the significant SNPs on 7A were located in a 0.19 Mb region containing 10 annotated genes near the region. A total of 444 significant SNPs were detected for fructan content on 21 chromosomes, each of which contributed the phenotypic variation from 8.9% to 13.9%. Of these, only three SNPs were detected in two environments. One SNPs were located on the 22.21 Mb on the chromosome 1A, two SNPs were located on the 677.53-677.83 Mb on chromosome 2A, and the significant SNPs on 2A were located in a 0.3 Mb region containing only one annotated genes. We will keep these further investigations for our future studies, with a view to finding new QTLs and genes associated with arabinoxylan and fructan content in wheat.