In rice production, pre-harvest sprouting (PHS) of late ripening seeds is one of the most serious quality defects in rice grain quality. In the present study, PHS impact was investigated by examining the physicochemical properties, eating and cooking quality (ECQ) of rice grain. Four rice cultivars suffering from PHS had impaired ECQ, reduced apparent amylose content, and decreased total starch content, with an increase in total protein content. The viscosity of flours and starches prepared from the PHS grains was significantly reduced. Starch molecular structure analysis also showed remarkable decreases in the short chains of amylopectin, long amylose chains and reduced starch crystallinity of the PHS grains. Moreover, the PHS native starch tended to have low starch digestibility. This provides useful information for understanding the effects of PHS on white rice grain quality as well as on starch fine structure and its physicochemical properties.