To study the microorganism for treating ammonia nitrogen in industrialized culture water at cold temperature, plate count method and most probable number were applied for quantitative detection of microorganism of the biological bead filter for treating ammonia nitrogen in a recycle culture system. At the same time, physical and chemical features of experimental team and controlled team were measured. The result showed that the amounts of nitrobacteria and nitrosobacteria increased continuously and they reached a stable level at anaphase. There were no denitrifying bacteria at the beginning of the experiment; its amount began to increase at anaphase. Comparing the concentrations of ammonia nitrogen, nitrate and nitrite of experimental team with that of controlled team, we can conclude that the biological bead filter for treating ammonia nitrogen runs well at 12℃. The experiment results indicate that the microorganism treatment, which is domesticated and induced at low temperature condition, is still a feasible approach to treat ammonia nitrogen in industrialized rainbow trout culture water at 12℃, which was deviated from the optimum microorganism growth temperature.