Understanding the energy/H₂O/CO₂ exchange processes is very important for evaluating the roles of tropical rain forest in climate change. The sensible heat, latent heat, and CO₂ fluxes above a tropical rain forest in Peninsular Malaysia were measured using the eddy covariance method for the year 2003. The diurnal patterns of energy, H₂O and CO₂ flux were investigated using a multi-layer model that considered patchy stomatal closure. Both bimodal and homogeneous stomatal opening distributions were simulated, and the results indicated that the observed negative relationship between CO₂ absorption under light-saturated conditions and vapor pressure deficit were not sufficiently explained by stomatal closure alone, for homogeneous stomatal opening distributions. For bimodal stomatal opening distributions, however, a greater depression in canopy photosynthesis was found with increased atmospheric vapor pressure deficit. These results strongly suggested that the depression in canopy photosynthesis was caused not only by stomatal closure limitation but also by the patchy (bimodal) stomatal behavior response to the increased atmospheric vapor pressure deficit. Thus, the midday depression in canopy photosynthesis was mainly caused by patchy (bimodal) stomatal closure.