<p>Salinity is a major problem due to the continuous increase in the salinization of agricultural lands, particularly, paddy fields. Using a forward genetics approach, salt-insensitive TILLING line 3, <i>sitl3,</i> was selected from a core population induced by gamma-ray irradiation. Under salt stress, <i>sitl3</i> had greater fresh weight and chlorophyll content, and lower H₂O₂ and Na⁺ contents than the wild-type. In the gene (<i>LOC_Os07g46180</i>) with two PWWP domains (named <i>Oyza sativa PWWP4</i>, <i>OsPWWP4</i>) of <i>sitl3</i>, a premature stop was caused by an SNP, and was named OsPWWP4p.Gly462* (a stop gain occurred from the 462th amino acid residue). The OsPWWP4 and substrate proteins (OsEULS2, OsEULS3, and OsEULD2) were identified using yeast two-hybrid, bimolecular fluorescence complementation, in vitro pull-down, and in vitro methyltransferase assays. Subcellular localization of OsPWWP4 and OsPWWP4p.Gly462*GFP-tagged proteins revealed they were both localized in the nucleus, while OsEULS2, OsEULS3, and OsEULD2 GFP-tagged proteins were found in the nucleus and cytosol of rice protoplasts. The expression levels of <i>OsEULS2, OsEULS3, OsEULD2</i> under salt stress were higher in <i>sitl3</i> than in wild-type plants. In contrast, <i>OsPWWP4</i> expression was higher in the latter. Genes involved in the salt overly sensitive (SOS) pathway showed higher expression in the aerial tissues of <i>silt3</i> than in the wild-type. CRISPR/Cas9-mediated <i>OsPWWP4</i> knock-out transgenic plants showed salt tolerance phenotypes with low Na⁺ contents and low Na⁺/K⁺ ratios. The data suggest that <i>sitl3</i> is a valuable genetic resource for understanding protein post-translational regulation-related salinity tolerance mechanisms such as methyltransferase activities, and for improving salt tolerance in rice through breeding.</p>