The objective of this study was to propose a model for explaining rice responses to a wide range of N application rates in various growth attributes associated with the occurrence of chalky grains. We improved the sub-model for N uptake process of a previous rice model which was originally developed for explaining genotypic and environmental variations in the whole growth processes, considering the difference in the rate of N loss from the plant-soil system between indigenously supplied soil mineral N and fertilizer N. A total of 80 growth datasets of cultivar 'Koshihikari' grown at Shiga prefecture, Japan, in 2010 was utilized for the calibration and validation of the model. The rice growth model well explained the above-ground biomass growth (RMSD = 78.7 g m(-2)) and rough dry grain yield (RMSD = 83.2 g m(-2)) for the validation data-set, simultaneously. The simulated carbohydrate content available per single spikelet was negatively correlated with the observed percentage of the milky-white grain which includes white-cored grain (r = -.77, p < .001) for all the data-sets of calibration and validation. On the other hand, the observed percentage of the sum of white-back and white-base grains was closely correlated with the simulated plant N content available per single spikelet (r = -.59, p < .001). It was suggested that the present rice growth model would rationally explain the effects of N application on the occurrence of the chalky grains through the dynamic change of the carbohydrate content and plant N content available per single spikelet.