Arabinoxylan (AX) and resistant starch (RS) are essential components of dietary fiber, that affect the nutritional value, health benefits, and end-use quality of wheat. Fully understanding their genetic basis is crucial for enhancing wheat quality through marker-assisted selection or other means. In this study, a genome-wide association study of AX-related traits i.e., total-arabinoxylan (TAX), water-extractable arabinoxylan (WEAX), and water un-extractable arabinoxylan (WUAX) of whole wheat flour (WWF) and refined wheat flour (RWF), as well as RS content was conducted using 205 elite wheat varieties (lines) with a composite map (24,355 SNPs) constructed with 90 K single nucleotide polymorphism (SNP) arrays. The broad-sense heritability (H2) of RS was 48.50%, whereas that of AX-related traits ranged from 55.66 to 77.23%. A total of 115 loci for RS and AX related traits, comprising 322 marker-trait associations (MTAs), were identified on all 21 chromosomes across four environments, explaining 5.52–12.40% of the phenotypic variance. Among them, 19 stable loci were significant in two or more environments, including one for RWF-TAX, six for RWF-WEAX, four for RWF-WUAX, three for WWF-TAX, two for WWF-WUAX, and three for RS. Furthermore, 17 co-located chromosomal regions related to the measured traits were stably detected in multiple environments. These findings may be used for further research and to improve wheat quality in wheat breeding programs.