Rice lipoxygenase 3 (OsLOX3) is a lipid hydroperoxidase found in rice embryos. Previous studies have reported that OsLOX3 is associated with seed quality and stress resistance, however, its relationship with grain shape and weight remains unknown. In this study, the first exon of OsLOX3 gene was edited in the indica rice variety GDR998 using CRISPR/Cas9 technology. Two homozygous mutants, Oslox3-1 (single-base deletion) and Oslox3-2 (single-base insertion) were identified among eight positive mutant plants from the T2 generation. The agronomic evaluation of genotypic OsLOX3 mutants showed significant increase in grain length, grain length-to-width ratio, 1000-grain weight, plant height, panicle length, and yield per plant compared with the wild type GDR998. The number of effective panicles and total grains per panicle did not significantly change. Further germination tests of seeds after three years of natural aging revealed that, compared with the control GDR998, the germination percentages of the mutants Oslox3-1 and Oslox3-2 increased significantly by 41.1% and 45.6%, respectively. These findings indicate that the knockout of OsLOX3 simultaneously improve grain weight and seed vigor, providing valuable germplasm resources for rice breeding targeting high-yield, improved seed longevity and rice quality.