Intensifying heat stress resulting from global warming threatens both the yield and quality of rice (Oryza sativa L.). Identifying pleiotropic genes that coordinately regulate yield, quality, and thermotolerance and applying them to rice breeding represents a promising strategy to mitigate the effects of high-temperature stress. Here, we identified Small Grain 9 (SMG9), which regulates grain size, grain chalkiness, and thermotolerance in rice. Map-based cloning indicated that SMG9 encodes a vernalization insensitive 4-like protein that is a component of Polycomb Repressive Complex 2. The smg9 mutant exhibited reduced grain size and chalkiness without compromised yield, and had improved thermotolerance during the flowering and seedling stages. By contrast, overexpressing SMG9 led to significantly larger grains, but resulted in inferior grain quality and increased thermosensitivity. Further study revealed that SMG9 positively regulates grain size by enhancing cell proliferation and cell expansion, and negatively regulates grain chalkiness by reducing reactive oxygen species (ROS) accumulation and delaying programmed cell death (PCD) in endosperm. Under natural high-temperature conditions, the loss of SMG9 function increased thermotolerance, thereby preserving both yield and grain quality. This enhanced thermotolerance at the seedling stage was also attributed to an improved ROS-scavenging capacity. Our study reveals the potential roles of SMG9 in maintaining yield and quality in rice under high-temperature conditions, offering a novel target gene for breeding thermotolerant rice.