CRISPR/Cas9-guided gene editing technology has become a popular and precision strategy in innovation of new plant germplasms and directional improvement of agronomic traits. The GS3 and qGL3 genes are the major regulating factors contributing rice grain elongation, and loss-of-function mutants result in enlarged grain size. To obtain new inheritable large grain rice germplasms, this study deployed CRISPR/Cas9 genome editing technology to edit GS3 and qGL3 genes in the japonica rice variety ‘Nanjing 5055’ showing small grain shape. Through agrobacterium-mediated genetic transformation of pYLCRISPR/Cas9 editing vector that carries GS3-gRNA and qGL3-gRNA, we obtained the GS3- and qGL3- edited plants, with the editing efficiency over 88%. In comparison with the wild-type ‘Nanjing 5055’, the GS3-edited lines showed about 9% increase on grain length, 12.5% increase on 1000-grain weight, as well as about 9.3% decrease on grain number per panicle. Interestingly, there was no significant difference in panicle number, panicle length, seed setting rate and yield per plant. For qGL3-edited lines, ca. 21.0% and 31.7% increases on grain length and 1000-grain weight, respectively, and ca. 31.5% decrease on grain number per panicle were observed. An increase on panicle number and a decrease on seed setting rate in qGL3 edited lines were detected if compared to those of ‘Nanjing 5055’, while no differences on panicle length and yield per plant were found. The contribution of qGL3 gene to grain shape and grain weight was significantly greater than those of GS3. Collectively, this study identified a series of new rice germplasms with enlarged grain size via genome editing of the GS3 and qGL3 genes in ‘Nanjing 5055’, which might have significant implications for grain size improvement in rice.