Percentage of grains with chalkiness (PGWC), one of the important traits assessing rice grain appearance quality, belonged to qualitative trait controlled by many genes. Our previous study identified a novel quantitative trait locus (QTL), namely qPGWC-9, related to high PGWC using chromosomal segment substitution line (CSSL) population. qPGWC-9 was shown to be expressed stably in eight environments. AIS82 which carried a IR24 chromosomal segment corresponding to qPGWC-9 in the Asominori genetic background was selected and analyzed to clarify the physiological function of qPGWC-9 from the relationship of source and sink of carbohydrates. It showed that AIS82 had higher PGWC than Asominori (control variety with low PGWC). The net photosynthetic rate of flag leaf of AIS82 showed no significant difference from that of Asominori, so photosynthetic ability in flag leaf was not directly related with high PGWC in AIS82. But, the changes in pattern of activity of the key enzymes associated with starch synthesis were different in these plants. Activities of some key enzymes in starch synthesis in AIS82 changed more radically than those in Asominori. These results suggest that qPGWC-9 might determine the activities of some enzymes associated with starch synthesis and therefore affect the degree of grain chalkiness.