To investigate the epigenetics dynamics during the synthetic process of the allohexapolyploid wheat, we generated the DNA methylomes of T. Urartu (AA), Ae. Longissimi(SS), and synthetic hexapolyploid wheat (SSAA) using MethylC-seq technology. We then used BS-Seeker2for BS-seq alignment, and CGmapToolsfor downstream data analysis. Each methylome is of high BS-conversion rate, and ~10X methylation-effective coverage. Interestingly, during the synthetic process, the whole-average DNA methylation levels decreased, and the differences of DNA methylation levels between AA and SS subgenomes are also decreased. The distribution of DNA methylations across the chromosomes in SSAA still kept the patterns as theirs in AA and SS, respectively. The correlation between DNA methylation levels and expression levels are different for distinct DNA methylation contexts, and gene functional regions. Differentially methylated regions (DMR) analysis showed more genes and regions in AA subgenomes are changed in DNA methylation than the numbers in SS subgenomes. The non-CG methylations patterns of SSAA are more likely to be inherited from AA subgenome original rather than SS subgenome. Our study provides a trial effort in understanding how the epigenetic modifications are coordinated between two subgenomes of the synthetic hexapolyploid wheat.