The synthesis of protein and starch in grain is crucial for regulating rice (Oryza sativa L.) chalkiness. However, little is known about how to coordinate them in the grain to improve the appearance quality of fragrant rice under nitrogen (N) fertilizer application. In the present study, both pot and field experiments were conducted to study the effects of N fertilization on chalkiness, starch and protein content, and enzyme activities related to carbon (C) and N metabolism in fragrant rice grains. The field experiment was carried out with five N levels of 0 (N0), 64 (N64), 128 (N128), 160 (N160), and 192 (N192) kg N ha−1, and a pot experiment was additionally performed with equivalent treatments. Compared to N0, N application significantly reduced fragrant rice chalkiness grain rate (17.54–39.47 %), chalkiness area (23.79–38.54 %), and chalkiness (35.98–61.27 %) in pot and field experiments. N fertilization decreased the mean grain filling rate (0.17 mg grain−1 d−1) and extended the effective grain filling duration (3.69 d). N fertilization significantly increased the protein content (16.17–22.63 %), which was driven by the improved activities of glutamine synthetase (GS), glutamate synthase (GOGAT), glutamic oxaloacetate transaminase (GOT), and glutamate pyruvate transaminase (GPT). Amylose and amylopectin contents, components of starch, decreased with N fertilizer application, which was associated with depression of the activities of adenosine diphosphate glucose pyrophosphorylase (AGP), granules bound starch synthase (GBSS), soluble starch synthase (SSS), and starch branching enzyme (SBE). The structural equation model (SEM) showed that N fertilization coordinated the synthesis of protein and starch and reduced the fragrant rice chalkiness by changing the process of C and N metabolism in fragrant rice grains. In short, the N fertilization decreased fragrant rice chalkiness by optimizing grain filling, balancing the protein and starch content in the grain.