•Increased temperature affects starch anabolism and further affected quality traits.•Under elevated temperature, nitrogen decreased the starch particle-size induced chalky rice.•Nitrogen regulates starch structure to further affect quality under elevated temperature.•Adjusting nitrogen fertilizer use likely mitigates quality deterioration under climate warming. Relevant evidence of rice quality responses to increased temperatures under field condition has been obtained in our previous study. Understanding the intrinsic mechanism of increased temperatures and fertilizer treatment in regulating rice quality formation will be contributed to the development of mitigation measures suitable for actual field operations and to cope with climate warming. This study investigated the potential role of nitrogen fertilizer in regulating the rice quality under field warming through identifying starch-related property indicators. Results showed application of nitrogen fertilizer at heading stage effectively delayed the significantly increased accumulation of total starch, amylose and amylopectin, and reduced the starch particle size, chain length distribution, and crystal structure induced by high temperature, which further compensated the deterioration of rice quality caused by elevated temperature.