Leaf photosynthetic nitrogen‐use efficiency (PNUE) diversified significantly among C3 species. To date, the morpho‐physiological mechanisms and interrelationships shaping PNUE on an evolutionary time scale remain unclear. In this study, we assembled a comprehensive matrix of leaf morpho‐anatomical and physiological traits for 679 C3 species, ranging from bryophytes to angiosperms, to comprehend the complexity of interrelationships underpinning PNUE variations. We discovered that leaf mass per area (LMA), mesophyll cell wall thickness (Tcwm), Rubisco N allocation fraction (PR), and mesophyll conductance (gm) together explained 83% of PNUE variations, with PR and gm accounting for 65% of those variations. However, the PR effects were species‐dependent on gm, meaning the contribution of PR on PNUE was substantially significant in high‐gm species compared to low‐gm species. Standard major axis (SMA) and path analyses revealed a weak correlation between PNUE and LMA (r2 = 0.1), while the SMA correlation for PNUE–Tcwm was robust (r2 = 0.61). PR was inversely related to Tcwm, paralleling the relationship between gm and Tcwm, resulting in the internal CO2 drawdown being only weakly proportional to Tcwm. The coordination of PR and gm in relation to Tcwm constrains PNUE during the course of evolution.