© 2018 The Author(s). In this study, we observed the change of the molecular structure of sugar chains in rice seeds at different growth stages after flowering using a confocal sum frequency generation (SFG) microscope. The sample was the rice kernel from "Nipponbare" (NIP) harvested at 3 days after flowering (DAF3). The SFG spectra were observed from 2 different positions on the cross section of the rice kernel seed. We detected amylopectin, a main ingredient of sugar chain contained in the rice seeds at DAF3, but the spectrum was a little different from that of normal amylopectin. By observing SFG spectra, we can investigate the structure of starch in the developing rice endosperm.