Drought stress is a significant environmental factor limiting crop growth worldwide. Malus prunifolia is an important apple species endemic to China and is used for apple cultivars and rootstocks with great drought tolerance. N6-methyladenosine (m6A) is a common epigenetic modification on messenger RNAs (mRNAs) in eukaryotes which is critical for various biological processes. However, there are no reports on m6A methylation in apple response to drought stress. Here, we assessed the m6A landscape of M. prunifolia seedlings in response to drought and analyzed the association between m6A modification and transcript expression. In total, we found 19,783 and 19,609 significant m6A peaks in the control and drought treatment groups, respectively, and discovered a UGUAH (H: A/U/C) motif. In M. prunifolia, under both control and drought conditions, peaks were highly enriched in the 3′ untranslated region (UTR) and coding sequence (CDS). Among 4204 significant differential m6A peaks in drought-treated M. prunifolia compared to control-treated M. prunifolia, 4158 genes with m6A modification were identified. Interestingly, a large number of hypermethylated peaks (4069) were stimulated by drought treatment compared to hypomethylation. Among the hypermethylated peak-related genes, 972 and 1238 differentially expressed genes (DEGs) were up- and down-regulated in response to drought, respectively. Gene ontology (GO) analyses of differential m6A-modified genes revealed that GO slims related to RNA processing, epigenetic regulation, and stress tolerance were significantly enriched. The m6A modification landscape depicted in this study sheds light on the epigenetic regulation of M. prunifolia in response to drought stress and indicates new directions for the breeding of drought-tolerant apple trees.