Nitrogen (N) application rates and planting density are key factors affecting grain yield and quality. In this experiment, four varieties, Huijing 753 (HJ 753), Huijing 855 (HJ 855), Huijing 866 (HJ 866), and Dangjing 8 (DJ 8), were used to investigate their effects on the yield and quality of japonica rice in Anhui, which has a lower soil N supply capacity. The current study set four levels of N application N1, N2, N3, and N4 (120, 180, 240, and 300) kg ha−1 and three planting densities D1, D2, and D3 (high-density: 45 × 104; medium-density: 37.5 × 104; low-density: 32.2 × 104) hills ha−1 for a total of 12 treatments. The effects of N application and planting density on rice yield, composition, processing quality, appearance quality, and cooking quality were analyzed. The results showed that with the increase in N application rates and planting density, the effective panicle number per plant and grain number per panicle of each rice variety increased, while HJ 753, HJ 855, and HJ 866 reached the highest yield under the N3D1 treatment and then gradually declined, and DJ 8 had the highest yield in the N4D1 treatment. In addition, the processing quality of various varieties can be improved by increasing the N application rate and planting density, but the appearance quality will deteriorate, the amylose content will also decrease, and gel consistency will also be lower. Therefore, under medium-planting density conditions, N at a rate of 240 kg ha−1 was the best for HJ 753, HJ 855, and HJ 866, and using 300 kg ha−1 for DJ 8 resulted in high grain yields and superior rice grain quality. In the next step, physiological, biochemical, and genotypic analyses of these three japonica rice varieties were carried out to provide a scientific basis and technical support for accelerating the breeding of high-yield japonica rice varieties.