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Nitrogen fertilizer is an important agronomic measure to regulate rice yield and grain quality. Grain filling is crucial for the formation of rice yield and grain quality. However, there are few studies on the effects of excessive nitrogen application (ENA) on grain filling rate and grain quality. A two-year field experiment was conducted to reveal the difference in grain filling characteristics and grain quality of superior grains (SG) and inferior grains (IG), as well as their responses to nitrogen fertilizer. We determined the grain appearance, the rice yield, the grain filling characteristics of SG and IG, and grain quality. We found that with the increasing nitrogen application level, grain yield of both varieties first increased and then decreased. The average yield of excessive nitrogen application (345 kg N ha−1) was 2.68–6.31% lower than that of appropriate nitrogen application (270 kg N ha−1). ENA reduced the grain filling rate by 12.7–25.8%, and the grain filling rate of SG was higher than that of IG. Increasing nitrogen application increased the processing quality and appearance quality of rice grain, but ENA deteriorated the appearance quality, eating quality and nutritional quality. The amylose content and taste value of SS were 3.1–9.7% and 7.1–20.2% higher than those of IS, respectively. The protein components of SG were lower than those of IG. Taken together, our results revealed that ENA leads to the lowering of rice grain yield and grain quality by suppressed grain filling of inferior grains.