The relationship between mean air temperature after heading and starch characteristics of colored rice grains was investigated using three colored rice cultivars. Pasting temperature within each rice cultivar with different harvest times differed. The pasting temperatures of two rice cultivars, Hongjinju and Joseongheugchal, reached the highest at 40 days after heading and decreased during the late harvest time. Distribution of amylopectin in the Hongjinju rice cultivar at the earlier harvest time contained a greater number of very short chains with the degree of polymerization (DP) between 6 and 12 and fewer chains with a DP from 13 to 24 than that of the later harvest time. However, there was little difference in the distribution of the longer chains of 25 ≤ DP ≥ 36 and 37 ≤ DP for latter harvest times compared to that of the earlier ones. It was suggested that the structure of amylopectin affected the varietal differences in patterns of chain length of amylopectin during grain filling. In addition, the control of ripening was different from that causing the pigment effects in the fine structure of amylopectin in the three colored rice cultivars. Larger starch granules were observed in the Joseongheugchal rice cultivar and smaller granules occurred in the Hongjinju rice cultivar. The present study revealed that later harvest times led to a clear increase in the mean granule size of starch in the three colored rice cultivars.