Heterosis is fundamental to modern tea breeding practices and is widely used in tea production. However, the epigenetic regulatory mechanisms underlying heterosis in tea plants remain relatively unknown. In this study, we integrated transcriptome, RNA methylation, and miRNA profile information to understand the epigenetic basis of heterosis in tea plants. We found that although m⁶A methylation modifications and miRNAs are highly conserved in tea plants, a significant number of differentially methylated and differentially expressed genes and differentially expressed miRNAs showed non-additive genetic effects in the hybrid. This non-additive expression is closely related to the synthesis of secondary metabolites and plant stress responses, implying that the regulation of these genes plays a key role in enhancing the quality and stress tolerance of hybrids. Through comprehensive analyses of the transcriptome, m⁶A methylation modifications, and miRNAs, we established a multi-level regulatory network, revealing the molecular mechanisms by which m⁶A methylation modifications and miRNAs drive heterosis in tea plants from the transcriptional to the post-transcriptional regulatory level. This multi-level regulatory network not only deepens our understanding of tea plant heterosis but also provides novel insights for further studies on the role of m⁶A methylation and miRNAs in tea plant heterosis.