The quality and starch properties of rice are significantly affected by nitrogen. The effect of the nitrogen application rate (0, 180, and 230 kg ha−1) on the texture of cooked rice and the hierarchical structure and physicochemical properties of starch was investigated over two years using two japonica cultivars, Bengal and Shendao505. Nitrogen application contributed to the hardness and stickiness of cooked rice, reducing the texture quality. The amylose content and pasting properties decreased significantly, while the relative crystallinity increased with the increasing nitrogen rates, and the starch granules became smaller with an increase in uneven and pitted surfaces. The proportion of short-chain amylopectin rose, and long-chain amylopectin declined, which increased the external short-range order by 1045/1022 cm−1. These changes in hierarchical structure and grain size, regulated by nitrogen rates, synergistically increased the setback viscosity, gelatinization enthalpy and temperature and reduced the overall viscosity and breakdown viscosity, indicating that gelatinization and pasting properties were the result of the joint action of several factors. All results showed that increasing nitrogen altered the structure and properties of starch, eventually resulting in a deterioration in eating quality and starch functional properties. A moderate reduction in nitrogen application could improve the texture and starch quality of rice while not impacting on the grain yield.