Late‐season rice, a major contributor to the production of high‐quality rice in China, often experiences low temperatures during the flowering period. The objective of this study was to determine the effect of low temperature stress on grain quality and to identify related physiological factors in late‐season rice. Sink and source characteristics and grain quality traits of two high‐quality late‐season rice cultivars were compared between a year in which low temperatures occurred during the flowering period (2020) and a normal year (2019) under field conditions. Low temperatures during the flowering period in 2020 resulted in a reduction in spikelet filling and consequent increases in source–sink ratios and grain weight and N content compared to 2019. The head rice rate and protein content of the milled rice were increased in 2020 compared to 2019. Starch gel consistency and peak, trough, breakdown, final, and consistency viscosities were reduced while setback viscosity, paste temperature, and texture properties (hardness, springiness, cohesiveness, resilience, and chewiness) were increased for milled rice (or milled rice flour or cooked milled rice) in 2020 compared to 2019. The glucose production rate and total glucose production from in vitro digestion of cooked milled rice was reduced in 2020 compared to 2019. The results of this study suggest that low temperature stress during the flowering period can improve milling, nutritional, and health qualities but reduce the cooking and eating quality in late‐season rice by altering the source–sink relationship.