Epitranscriptomic chemical modifications of RNAs have emerged as potent regulatory mechanisms in plants. Owing to the technical advances in detecting RNA modifications and high-throughput sequencing, our understanding of the diversity and landscape of RNA modifications across organisms has been significantly improved, resulting in the birth of the epitranscriptome that focuses on deciphering the function of RNA modifications. Currently, more than 170 distinct chemical modifications have been identified in mRNAs, tRNAs, rRNAs, and noncoding RNAs (ncRNAs). RNA modifications include N6-methyladenosine (m6A), 1-methyladenosine (m1A), 5-methylcytosine (m5C), 3-methylcytosine (m3C), 7-methylguanosine (m7G), pseudouridine (Ψ), and so on. Genetic and molecular studies have identified the genes responsible for the addition, interpretation, and removal of chemical modifications from RNA molecules, which are known as “writers”, “readers”, and “erasers”, respectively. RNA modifications play important roles in gene expression regulation by regulating mRNA stability, protein translation efficiency, splicing of mRNA or pri-miRNAs, and mRNA nuclear exporting. RNA modifications are widely involved in plant growth, development, stress response, crop yield, and immune response. Thus, further investigation into the distribution patterns and functional mechanisms of RNA modifications will deepen our understanding of RNA modification biology from the perspective of epitranscriptomics and provide new strategies for potential applications in plants and future improvement of crops.