N6-methyladenosine (m6A) is one of the most prevalent post-transcriptional modifications in mRNA, tRNA, miRNA, and long noncoding RNAs in eukaryotes, which play the diverse RNA-regulatory roles in many biological processes. However, the genome-wide map of the m6A in wheat (Triticum aestivum L.) and its potential biological functions in response to drought stress has not been well studied. In this study, we revealed a potential link between m6A deposition and PEG-induced drought stress by parallel m6A immunoprecipitation sequencing (m6A-seq) and RNA-seq analysis. Totally, 4,221 m6A peaks and 3,733 m6A-related genes were obtained, of which 373 methylated sites in genes were differentially expressed between CK and stressed treatment. Similar to Arabidopsis, m6A loci in the wheat transcriptome were also significantly enriched around stop codons and within 3 untranslated regions (3'UTRs). m6A-seq and RNA-seq analysis showed a positive association between m6A methylation and mRNA abundance. GO and KEGG enrichment results showed that differential genes in both m6A and mRNA levels were significantly associated with photosynthesis and metabolism processes. Interestingly, one m6A-binding protein (TaETC9) displayed significantly up-regulated expression and one m6A demethylase (TaALKBH10B) gene was significantly down-regulated expressed under drought stress, which might contribute to the increased m6A levels under drought stress. We further validated these changes in m6A and mRNA levels through gene-specific m6A-IP-QPCR and normal QPCR. This study reported the first m6A profile of wheat under PEG-induced drought stress, which provided a foundation for further revealing the potential role of RNA methylation underlying stress response and also contribute to genetic improvement of stress tolerance based on the epigenetic approach in wheat.