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N⁶-methyladenosine (m⁶A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m⁶A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m⁶A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m⁶A methylation in the shoots (<i>p</i> value < 0.05). Additionally, 2537 and 2304 differential m⁶A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m⁶A sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased m⁶A methylation levels only in the shoots or roots under salt stress, implying m⁶A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m⁶A modifications and gene expression changes revealed that m⁶A changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of m⁶A modifications on rice salt tolerance.