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After transcription, a messenger RNA (mRNA) is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N⁶-methyladenosine, m⁶A). Both RNA secondary structure and m⁶A have been demonstrated to regulate mRNA stability and translation and have been independently linked to plant responses to soil salinity levels. However, the effect of m⁶A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure is highly dynamic during salt stress, and that it is independent of changes in RNA-protein interactions. Conversely, we find that m⁶A is anti-correlated with RNA secondary structure in a condition-specific manner, with salt-specific m⁶A resulting in a decrease in mRNA secondary structure during salt stress. Remarkably, we show that the combination of salt-specific m⁶A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability and translation of transcripts encoding proteins involved in responses to abiotic stresses. In total, our comprehensive analyses reveal important post-transcriptional regulatory mechanisms involved in plant long-term salt stress response and adaptation.