The nitrogen application rate strongly influences the eating quality (EQ) of rice. However, the starch molecular structure mechanism underlying the differences in taste quality between superior (SG) and inferior grains (IG) and their response to nitrogen application rates must be further studied. In this study, the starch molecular structure (SMS), starch physicochemical properties (SPP) and EQ of SG and IG were determined under four nitrogen application rates (N1:0, N2:195, N3:270 and N4:345 kg ha−1). We found that the SMS-related indicators of excessive nitrogen application (ENA, N4) were 8.45%–32.59% lower than those of N1. ENA decreased the EQ by 11.2%–30.3%. ENA has a strong influence on both the SMS and SPP. The fa and (fa + fb1)/(fb2 + fb3) of ENA were significantly greater than those of N1. ENA decreased the percentage of A and B chains by 11.2–47.2% and increased the percentage of C chains by 46.8–80.6%. Correlation analysis revealed that the amylose chain length distribution was closely related to the rice EQ. The SMS and SPP of IG were more sensitive to the ENA. The relatively high contents of C chains and fb1 in IG contribute to poor EQ. In summary, the starch physicochemical properties and molecular structure of IG are more susceptible to the effects of ENA, resulting in poor EQ.