The replacement of common urea with controlled-release nitrogen fertilizer can improve rice yield and quality, but the effect of controlled-release nitrogen fertilizer on rice yield and quality at different release stages is still unclear. In this experiment, two nitrogen application rates (240 kg/ha and 300 kg/ha) and five different nutrient release characteristics (urea and coated urea with controlled release periods of 30, 50, 70 and 90 days, respectively) were set up to explore the effects of nitrogen application rate, release characteristics and their interactions on rice yield, quality, starch structure, and physicochemical properties. The results showed that, compared with other controlled-release nitrogenous fertilizers, application of controlled-release nitrogenous fertilizers for 30 days and 90 days could increase rice yield (14.17% to 20.83%), and application of controlled-release nitrogenous fertilizers for 70 days and 90 days had the highest comprehensive evaluation of rice quality. The decrease of amylose content and the increase of protein content significantly improved the eating and nutritional quality of rice by changing the structure and physicochemical properties of starch particles. The results showed that in the comprehensive evaluation system based on rice yield and quality, under the condition of 300 kg/ha, controlled-release nitrogen treatment with a controlled release period of 90 days had the highest comprehensive score, which could increase rice yield and improve grain quality.