The invention discloses a polymorphic microorganism aggregate autotrophic nitrogen removal integrated device which is provided with a reaction tank, wherein the reaction tank is internally filled with microorganism aggregates and is provided with a water decanting device with a vertical push rod, fixed packing, an aerator, an online pH value detector, an online dissolved oxygen detector, an online ammonia nitrogen detector and an online nitrate nitrogen detector; the reaction tank is connected with a water inlet pipeline, a water outlet pipeline, a sludge outlet pipeline, an air pipeline, an overflow pipeline, a water inlet pump, a blast blower and an electrically operated valve; the reaction tank is also provided with an online gas flowmeter and a PLC (Programmable Logic Controller); the online gas flowmeter, the online pH value detector, the online dissolved oxygen detector, the online ammonia nitrogen detector and the online nitrate nitrogen detector are all connected with the PLC through signals. An operation method comprises the steps: (1) inoculating sludge; (2) carrying out habituated culture; (3) starting partial nitrification reaction; (4) inoculating anaerobic ammonium oxidization granular sludge; (5) proliferating the anaerobic ammonium oxidization granular sludge; (6) culturing an anaerobic ammonium oxidization bacterium biological film; (7) stably operating the autotrophic nitrogen removal integrated device. The polymorphic microorganism aggregate autotrophic nitrogen removal integrated device is suitable for denitrification treatment of medium and high concentration ammonia nitrogen sewage, simple in structure, high in degree of automation, good in denitrification effect and low in operation cost.