Reduced mesophyll conductance induces photosynthetic acclimation of japonica rice under elevated CO2

•Using quantitative analysis to explore mechanism of photosynthetic acclimation in japonica rice under elevated CO2.•Mesophyll conductance was the primary contributor to photosynthetic acclimation, accounting for 65 % across the developmental stages.•Research also showed the association of leaf nitrogen with mesophyll conductance and stomatal conductance.