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Nitrogen management (nitrogen application ratio in transplanting, tillering, and panicle initiation growth stages) is an important parameter in crop cultivation and is closely associated with rice yield and grain quality. The physicochemical and structural properties of starches separated from two rice varieties grown under four different nitrogen management ratios (0; 9:1; 7:3; 6:4) were investigated. As the percentage of fertilizer used in the panicle initiation stage increased, the content of small granules increased while the content of large granules decreased, the decreased amylose content resulting high selling power, water solubility, gelatinization enthalpy and low retrogradation. The crystallinity of the starch samples was found to be A-type. This study indicated that the best nitrogen management ratio for the cultivation of rice with the highest yield, desirable starch physicochemical properties for high quality cooked rice, and a moderate protein level was 7:3.