<p>Internal chemical modifications of mRNA constitute a key epitranscriptomic layer of gene regulation in eukaryotes. Although <i>N</i>⁶-methyladenosine (m⁶A) has been the most intensively studied, accumulating evidence reveals important roles of non-m⁶A mRNA modifications, such as 5-methylcytosine, <i>N</i>⁴-acetylcytidine and pseudouridine, in plants. These modifications modulate diverse aspects of mRNA metabolism, including alternative splicing, stability, translation and long-distance transport, and thereby shape plant development and environmental adaptation. Here we summarize current advances in understanding non-m⁶A mRNA modifications in plants, emphasizing their regulatory roles in mRNA metabolism and their effects on plant development and stress resilience. We also review the detection technologies for non-m⁶A modifications and discuss key challenges and future directions towards elucidating their regulatory functions.</p>