AbstractA coordinated increase in the photosynthetic rate (A) and photosynthetic nitrogen use efficiency (PNUE) is an effective strategy for improving crop yield and nitrogen (N) utilization efficiency. PNUE tends to decrease with increasing N levels, but there are natural variations. Consequently, leaf functional N partitioning in Brassica napus genotypes under different N rates was measured to explore the optimized N allocation model for synchronously increasing A and PNUE values. The results showed that genotypes whose PNUE increased with increasing N supply (PNUE‐I) produced an approximate A value with a relatively low leaf N content, owing to reduced storage N (Nstore) and close photosynthetic N (Npsn) content. Partial least squares path modeling showed that A was dominated by the Npsn content, and PNUE was directly influenced by A and Nstore. The A value increased with the Npsn content until the Npsn content exceeded the threshold value. The boundary line of PNUE varied with the Npsn and Nstore proportions, indicating that the optimum Npsn and Nstore proportions were 51.6% and 40.3%, respectively. The Nstore proportion of PNUE‐I was closer to the thresholds and benefited from lower increments in Rubisco content and nonprotein form storage N content with improved N supply. Optimized Nstore and Npsn trade‐off by regulating increments in Nstore content with increased N supply, thereby promoting coordinated increases in A and PNUE.