Southeast Asian tropical rain forests are among the world's most important biomes in terms of global carbon cycling; nevertheless, the impact of environmental factors on the ecosystem CO2 flux remains poorly understood. One-dimensional multilayer biosphere-atmosphere models such as soil-vegetation-atmosphere transfer (SVAT) models are promising tools for understanding how interactions between environmental factors and leaf-level physiological parameters might impact canopy-level CO2 exchange. To examine application of the SVAT model in tropical rain forests, which is expected to be difficult partly because of the complex canopy structure and large number of tree species, we measured vertical and horizontal variations in leaf-level physiological parameters and leaf area densities together with eddy covariance measurements using a canopy crane in a tropical rain forest in Sarawak, Malaysia. Despite differences in species and canopy positions, leaf nitrogen per unit area (Na) within the canopy could be one-dimensionally described as a linear function of height. Na also clearly explained the other leaf-level physiological parameters across species and canopy positions. Even though the leaf area density profile likely varies in this tropical forest, the SVAT model satisfactorily reproduced the eddy covariance measurements. Furthermore, the CO2 flux calculated on the assumption that Na measured in the upper canopy was distributed evenly throughout was almost the same as that taking the vertical gradient into consideration. These findings suggest that when reproducing the CO2 flux in tropical rain forests using the SVAT model, the leaf area density profile obtained from the leaf area index (LAI) measured at one point and leaf-level physiological properties measured across species in the upper canopy are sufficient.