Granulation is an important class of production processes in food, chemical and pharmaceutical manufacturing industries. In urea fertilizer manufacturing, fluidized beds are often used for the granulation system. However, the granulation processes release ammonia to the environment. Ammonia gas can contribute to eutrophication, which is an oversupply of nitrogen and acidification to the ecosystems. Eutrophication may cause major disruptions of aquatic ecosystems. It is estimated that global ammonia emissions from urea fertilizer processes are approximately at 10 to 12 Tg N/year, which represents 23% of overall ammonia released globally. Therefore, accurate modeling of the ammonia emission by the urea fertilizer fluidized bed granulation system is important. It allows for the system to be operated efficiently and within sustainable condition. This research attempts to optimize the model of the system using the particle swarm optimization (PSO) algorithm. The model takes pressure (Mpa), binder feed rate (rpm) and inlet temperature (°C) as the manipulated variables. The PSO searches for the model’s optimal coefficients. The accuracy of the model is measured using mean square error (MSE) between the model’s simulated value and the actual data of ammonia released which is collected from an experiment. The proposed method reduces the MSE to 0.09727, indicating that the model can accurately simulate the actual system.