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Grain filling is an extremely important process in rice growth and development. This process which involves complex genetic regulatory networks and environmental interaction, is directly related to the formation of rice yield and quality. A stable inherited mutant with grain extended filling ( gef1 ) was identified from an EMS mutagenized population of Yixiang 1B. The investigation of agronomic traits, measurement of physiological and biochemical characteristics, histology observation, gene expression analysis and gene mapping were performed in this study. Compared with the wild type plants, the grain filling rate of gef1 was significantly lower than that of Yixiang 1B, resulting in the grain filling time of gef1 was about 30 days delay. Meanwhile, the 1000-grain weight of gef1 became bigger and seed setting rate decreased by 22%. During the development of caryopsis, we found that the soluble sugar content in wild type showed a single peak curve, and the content maintained at a low level throughout the grain filling stage. However, the soluble sugar content of the gef1 was significantly higher than that of the wild type, and showing a bimodal curve. It revealed that the transportation and distribution of photosynthate, and starch synthesis were inefficiency in gef1 . In addition, histocytological analysis showed that the number of big vascular bundles in the same transection parts of rachis, the first top internodes and the second top internodes were all decreased in gef1 , and indicated that the transport efficiency of photosynthate was one of the limiting factors in the rate of grain filling. The scanning electron microscope showed that the glume of gef1 had smooth surface and slender cells. Scanning of grain transection showed that gef1 had spherical amyloplasts and arranged loosely, but the wild type had unregular polygon amyloplasts and packed closely. These results suggested that the changes of grain size associated with the cell number and shape of glume, and gef1 had impact on rice quality. Additionally, by analyzing the expression of the glycometabolism-related genes in developing caryopsis, we found that all of them were keeping at a low level in gef1 compared with the wild type. By analyzing the three crosses gef1 /Yixiang 1B, gef1 /02428 and gef1 /Kitaake, we found that the F1 plants of these three crosses were all normal and indicated that the mutant trait was controlled by a recessive gene. The ratio of normal plants to mutant plants in the three F2 populations was 3:1 and indicating that the mutant trait was controlled by a single recessive nuclear gene. gef1 was preliminarily mapped on the short arm of rice chromosome 3, and was narrowed to a 198 kb region between InDel3-1 and InDel3-2. This region has 21 open reading frames and there was no homologous gene had been reported within it, and the further identification work of candidate genes is ongoing.