The invention belongs to the treatment field of waste water, and provides a method for converting active sludge into autotrophic denitrified sludge based on a mixed type continuous flow reactor. The method which is used for converting the common active sludge into the autotrophic denitrified sludge by the continuous flow reactor specifically comprises two stages. The first stage comprises the steps of: converting anaerobic or anoxic sludge into a nitrosation status by the condition which controls the organic matter concentration (COD (chemical oxygen demand) is less than 20mg/L), the water dissolved oxygen concentration (1-0.5mg/L), and the inflowing ammonia nitrogen concentration (50-450mg/L), and restraining the growth of the other microorganisms step by step by the running condition and the washing characteristic of the continuous flow reactor. When the cumulative percentage of the nitrite is more than 60%, the second stage is started. The second stage comprises the step of: promoting the nitrosation status to be converted into the autotrophic denitrification status by the condition which improves the ammonia nitrogen concentration (450-550mg/L), reduces the dissolved oxygen (0.5mg/L), and keeps a certain PH value (7.5-8.0) to form a system which is coupled nitrosified microorganism to anammox microorganism. The practice proves that the system can stably run for a long term. After entering into the practical running stage of the waste water treatment, the method leads the ammonia nitrogen removing rate and the total nitrogen removing rate to be respectively more than 80% and 70% by the reaction which is remained only by the natural reoxygenation or a small quantity of aeration without aeration.