Indica–japonica hybrid rice (I–JR) typically has greater grain yield than that of Indica hybrid rice (IR) under prolific shading, but it is not known how shading impacts on physiological characteristics underpinning grain quality. Here, we conducted a two-year field experiment in the mid-reaches of the Yangtze River region using I–JR (genotypes Yongyou 1540 and Yongyou 538) and IR (genotypes Y-liangyou 900 and Quanyouhuazhan). We found that shading reduced grain appearance and quality, particularly milling and heading rates, and chalkiness. Shading disrupted carbon and nitrogen metabolism, impacting traits influencing the human perception of the taste of the grain, such that amylose decreased by 5.9% (I–JR) and 12.9% (IR); grain protein significantly increased, with lesser effects in I–JR than IR under shading. Shading also reduced peak, hot, and final viscosities, and breakdown value. I–JR had improved rice quality compared with that of IR due to the greater propensity of the former to photosynthesize under shading, leading to the improved functioning of carbon and nitrogen metabolism.