<p>The epigenomic landscape regulates gene expression and chromatin dynamics, with histone and RNA modifications playing crucial roles. Although studies have elucidated the interactions among chromatin modifications, DNA methylation, and mRNA modifications, the relationships among RNA modifications and their collective influence on RNA metabolism remain poorly understood. Grasping these epigenetic mechanisms is essential for improving crop resilience and productivity. In this study, we explored the co-occurrence and functional interactions of three significant mRNA modifications in Arabidopsis (<i>Arabidopsis thaliana</i>) and rice (<i>Oryza sativa</i>): <i>N</i>^<i>4</i>-acetylcytidine (ac⁴C), <i>N</i>^<i>6</i>-methyladenosine (m⁶A), and 5-methylcytosine (m⁵C). Our results indicate that these modifications frequently coexist in the same transcripts, exhibiting distinct spatial distributions across species. Notably, the m⁶A modification enhances the ac⁴C-mediated destabilization of RNA secondary structures, especially when modifications are clustered, thereby promoting RNA stability. In Arabidopsis, the ac⁴C modification improved translational efficiency and the m⁶A modification amplified this effect in a distance-dependent manner; by contrast, in rice the influence of m⁶A is independent of distance. The m⁵C modification has minimal impact on RNA structure or stability but modulates m⁶A-associated transcript stability in a context-dependent manner. Our findings shed light on the dynamic regulatory code of combinatorial RNA modifications, highlighting species-specific mechanisms of post-transcriptional regulation. This research offers valuable insights into the intricate interplay of RNA modifications, with implications for advancing agricultural biotechnology through a deeper understanding of plant RNA functionality.</p>