Chalkiness, one of the key factors in determining the market price and quality of rice grains, is markedly influenced by the environment. This study aimed to investigate the effectiveness of shading on rice chalkiness by conducting a field experiment in Wenjiang, Sichuan, China, in 2013 and 2015. Rice cultivars IIyou 498 and Yixiangyou 2115 were selected and shaded during the grain filling period; this resulted in a 53% shading environment. The results showed that chalkiness, caryopsis and amyloplast development, amylose content, and amylopectin chain-length distribution of rice grains, were markedly affected by shading. Shading significantly increased chalky rice rate and chalkiness degree of rice grains at the bottom of the panicle, which contributed to the increase in chalkiness of the entire panicle. Shading had a greater influence on grains at the bottom spikelet positions than on those at the top and middle positions. More loosely packed amyloplasts with greater airspace and reduction in amylose content of grains at the bottom spikelet positions were possibly due to the significant delay in the development of caryopsis. Furthermore, except for the bottom spikelet positions of Yixiangyou 2115, a reduction in short-length chains coupled to an increase in long-length chains of amylopectin was noted under shading. Shading increased rice chalkiness primarily by postponing caryopsis development at the bottom spikelet positions and disturbing the starch characteristics of rice grains. Therefore, more attention needs to be focused on the grains positioned at the bottom of panicle.