DNA methylation is an important epigenetic modification that may contribute to environmentally induced phenotypic variations by regulating gene expression. Chemically induced male sterility (CIMS) lines in wheat (Triticum aestivum L.) can transform from sterile to fertile, induced by a chemical hybridising agent during anther development. So far, little is known about the DNA methylation variation of CIMS in wheat. TAA1 regulates pollen wall development, probably through converting fatty acids to fatty alcohol in wheat. We investigated the DNA methylation pattern of the TAA1 gene in the core promoter region by using the bisulfite genomic sequencing method, and higher methylation was observed in CIMS. The expression levels of the TAA1 gene were also evaluated by real time quantitative reverse transcriptase PCR analysis, which revealed that the expression levels of the TAA1 gene were downregulated in CIMS. The aliphatic composition of the anther underwent accumulation in line 1376-CIMS, revealed by gas chromatography–mass spectrometry, including increments of tetradecanoic acid, hexadecanoic acid and octadecanoic acid. Scanning electron microscopy revealed that anther and pollen wall formation was significantly altered in 1376-CIMS.These results suggested that DNA methylation of the TAA1 gene may be involved in the sterility–fertility transition of CIMS.