RNA 5-methylcytosine (m5C) modification is involved in various developmental processes and stress tolerance. However, its role in abiotic stress responses remains largely unknown in rice. We previously demonstrated that the writer OsNSUN2 is required for heat adaptation by facilitating the translation of m5C-mRNAs. Herein, we identify OsALY4 as an m5C reader to modulate the chilling and salt tolerance in rice seedlings. The interaction between OsALY4 and RNA helicase OsAIP2 is essential for nucleocytoplasmic export of target mRNAs of OsALY4 under normal condition, including those of OsWRKY45, OsMDHAR3, and OsHAK13. In the osaly4 mutant, these target mRNAs are more efficiently transported to cytoplasm under stress conditions due to the high expression of OsALY2 and OsALY6, which affect chilling and salt tolerance through several pathways. Our findings uncover the critical function of m5C modification on mRNA transport and stress adaptation in rice, shedding new light on the intricate mechanisms underlying plant resilience.