DNA and histone modifications have notable effects on gene expression(1). Being the most prevalent internal modification in mRNA, the N-6-methyladenosine (m(6)A) mRNA modification is as an important post-transcriptional mechanism of gene regulation(2-4) and has crucial roles in various normal and pathological processes(5-12). However, it is unclear how m(6)A is specifically and dynamically deposited in the transcriptome. Here we report that histone H3 trimethylation at Lys36 (H3K36me3), a marker for transcription elongation, guides m(6)A deposition globally. We show that m(6)A modifications are enriched in the vicinity of H3K36me3 peaks, and are reduced globally when cellular H3K36me3 is depleted. Mechanistically, H3K36me3 is recognized and bound directly by METTL14, a crucial component of the m(6)A methyltransferase complex (MTC), which in turn facilitates the binding of the m(6)A MTC to adjacent RNA polymerase II, thereby delivering the m(6)A MTC to actively transcribed nascent RNAs to deposit m(6)A co-transcriptionally. In mouse embryonic stem cells, phenocopying METTL14 knockdown, H3K36me3 depletion also markedly reduces m(6)A abundance transcriptome-wide and in pluripotency transcripts, resulting in increased cell stemness. Collectively, our studies reveal the important roles of H3K36me3 and METTL14 in determining specific and dynamic deposition of m(6)A in mRNA, and uncover another layer of gene expression regulation that involves crosstalk between histone modification and RNA methylation.