Rice is a significant staple crop, with salinity being a primary abiotic stress leading to reduced yields. Improving rice alkaline tolerance to expand cultivation areas is vital for boosting total production and securing food supply. In this study, a mutant with significantly reduced alkaline tolerance was identified from the γ-ray induced mutation library of the Geng/japonica rice variety Sasanishiki (WT). The target gene was located in an 87.7 kb region between P2 and P3 on chromosome 11, containing nine open reading frames (ORFs) through map-based cloning. Sequence comparison revealed a deletion of four bases in the third exon of ORF9 in the mutant, leading to premature termination of the gene. Therefore, ORF9 is hypothesized to be the candidate gene responsible for reduced alkaline tolerance and has been named Alkaline Tolerance 11 (AT11). AT11 encodes a putative peptide transporter (PTR). Transgenic experiments showed that CRISPR/Cas9 knockout lines of AT11 weakens alkaline tolerance, whereas its overexpression significantly enhances alkaline tolerance. AT11 is expressed in all tissues of rice, with the highest expression in the panicle. Yeast two-hybrid and Immunoprecipitation assays revealed that AT11 can interact with GS3, the heterotrimeric G-protein γ subunit in rice. Bimolecular fluorescence complementation experiments show that AT11 and GS3 interact on the plasma membrane. Transcriptome sequencing revealed that the differentially expressed genes between WT and AT11 knockout lines were significant enriched in pigment binding and photosynthesis. Yield testing under field conditions at pH 9.0 showed that overexpressing AT11 significantly increases yield, demonstrating that AT11 can enhance the productivity of rice on saline-alkaline soils, with potential salt alkaline resistance broad breeding application prospects.