Grain shape is one of the important traits to evaluate rice yield and quality. Understanding the molecular mechanism is great important for genetic improvement of the rice variety (Oryza sativa). In this study, we used EMS to generate a population of M2 seedling from a japonica rice variety, ‘TB309’, and sieved a mutant performing dwarf and small grain (dsg1) compared with the wild type. Mature dsg1 plants were shorter with fewer tillers. The spike length and internode distances were reduced, resulting in a 20.35% in plant height. The grain length of dsg1 were 15.53% shorter, 7.26% wider and 10.45% thicker than of ‘TB309’ grains. The phenotypic variation of grain length in F2 population derived from dsg1 with ‘9311’ performed a segregation ratio of 3:1, revealing that dsg1 mutant phenotype is due to the recessive mutant of a single locus. Through the phenotypic performance of extremely recessive individuals, the candidate was directly narrowed to a 52.28-kb region between ID2798 and ID2803 on the long arm of chromosome 4. Based on the information from Gramene database, we identify total 11 genes in this region. Together, our presented results prove a potential foundation for further molecular function analysis of the responsible gene.