In this study, 205 elite wheat lines from winter wheat region of China were used as materials to analyze the phytic acid content, and the cluster analysis and related was further conducted. The results showed that the average Phytic acid content of the two environmental groups was 4.99 g/kg and 3.31 g/kg, and the variation range was 17.90 g/kg and 10.20 g/kg, respectively. The variation range was relatively large. The results of cluster analysis showed that there were significant differences in Phytic acid content among 6 groups. B54, B40, B86 and B126 have the lowest phytic acid content among the extended varieties or backbone parents, which can be used as important parents in low Phytic acid wheat breeding. The higher generation lines B131, B141, B181 and B149 had the lowest phytic acid content. Combined with excellent agronomic traits, it is expected to select new functional wheat varieties with low Phytic acid content. A total of 36 single nucleotide polymorphism (SNP) markers associated with phytic acid content in wheat grains were detected (P < 0.001), which were distributed on chromosomes 2B, 3A, 3B, 3D, 6A and 6B. The contribution rate of phenotypic variation of a single Association site was 5.73% ~ 9.69%.Excellent alleles of genes with low Phytic acid content were identified such as tdurum, were identified_contig35799_208-G、Excalibur_c96134_152-C and tdurum_contig43538_1687-A, etc. which had a greater effect on low Phytic acid content.