The study was carried out to develop a mathematical model for evaluating the effect of organic fertilizers in organic rice production systems. A function to simulate the nitrogen mineralization process in the paddy soil has been developed and integrated into ORYZA2000 crop growth model. Inorganic nitrogen in the soil was estimated by single exponential models, given temperature and C:N ratio of organic amendments. Data collected from the two-year field experiment were used to evaluate the performance of the model. The revised version of ORYZA2000 provided reasonable estimates of key variables for nitrogen dynamics and crop growth in the organic rice production systems. Coefficient of determination between the measured value and simulated value were 0.6613, 0.8938, and 0.8092, respectively for soil inorganic nitrogen, total dry matter production, and rice yield. This means that the model could be used to quantify nitrogen supplying capacity of organic fertilizers relative to chemical fertilizer. Nitrogen dynamics and rice growth simulated by the model would be useful information to make decision for organic fertilization in organic rice production systems.