A primary focus of rice breeding and production is the optimization of yield and quality. Currently, semi-waxy japonica rice is widely planted in the middle and lower reaches of the Yangtze River due to its good eating quality and strong reputation among consumers. However, little information is yet available on grain yield formation and rice quality characteristics of these semi-waxy japonica rice varieties with different grain yields. In this study, three high-yielding (HGY) semi-waxy japonica rice varieties and three low-yielding (LGY) semi waxy japonica rice varieties were compared for population quality and rice quality in 2018 and 2019. The average values of spikelet per panicle, 1000-grain weight, and total spikelet number of the HGY varieties were significantly higher than those of the LGY varieties, while the panicle number and filled grain rate showed the opposite. Compared with the LGY varieties, the HGY varieties had a larger leaf area index at each growth stage, with a larger high efficient leaf area composed of a larger leaf length and width and smaller leaf angles of the top three leaves, as well as a greater single stem-sheath weight, more total dry matter accumulation, and longer growth duration from elongating to maturity. There were significant differences in rice quality between the HGY and LGY varieties. Compared with the LGY varieties, the head milled rice rate of the HGY varieties decreased significantly, and the chalky kernel rate and chalkiness degree increased significantly. Due to the low protein content, high peak viscosity, trough viscosity, and final viscosity and breakdown, as well as low setback, consistence, and pasting temperature of the HGY varieties, their taste values were significantly better than those of the LGY varieties. These results suggest that the HGY varieties could achieve a synergistic improvement of grain yield and eating quality, but the milling quality and appearance quality require further improvement.