Using Zhengdao C42 and Xudao 3 as test varieties, four nitrogen(N) application rates were set: 0 kg/hm2(N0), 120 kg/hm2(N120), 240 kg/hm2(N240), and 360 kg/hm2(N360). The differences of milling quality, appearance quality, cooking and nutritional quality, contents of certain organic acids and hormones in root exudates, and root anatomical structure were measured. Results showed that brown rice rate, milled rice rate, head rice rate, gel consistency, and the contents of tartaric acid, acetic acid(except during the initial stage of panicle differentiation in Xudao 3), zeatin and zeatin riboside(Z+ZR) in the root exudates of the two varieties of rice initially increased and then decreased with higher N rates, peaking at N240. In contrast, contents of amylose, oxalic acid, citric acid, alkali spreading value, and the ratio of stele diameter to root diameter initially decreased and then increased, reaching their lowest values at N240. For Xudao 3, cortical cross-sectional area, stele diameter, and root diameter peaked at N240. For Zhengdao C42, the proportion of living cells peaked at N240, while cortical cross-sectional area, stele diameter, and root diameter peaked at N360, with no significant difference between N360 and N240. Contents of Z+ZR, tartaric acid, acetic acid, succinic acid in root exudates, and living cell proportion were significantly positively correlated with milled rice rate, head rice rate, protein content, and gel consistency of rice. Aerenchyma area, cortical cross-section, stele diameter, and root diameter were significantly positively correlated with appearance quality, while oxalic acid content and the stele-to-root diameter ratio were significantly negatively correlated. At 240 kg/hm2 N, processing, cooking, and nutritional quality improved: Xudao 3 showed increases of 7.7%, 18.4%, and 45.9% in brown rice, milled rice, and head rice rates, respectively, and Zhengdao C42 increased by 14.6%, 14.7%, and 36.0%, while amylose contents decreased by 14.2% and 20.0%, alkali spreading value decreased by 11.2% and 11.6%, and gel consistency increased by 10.2% and 5.7% for Xudao 3 and Zhengdao C42, respectively.