The invention discloses a device and a method for denitrification of single stage autotroph in low-cellulose nitrate (CN) high-ammonia nitrogen waste water. The device comprises a raw water tank, a water inlet pump, a reactor, a secondary sedimentation tank and a sludge reflux pump, wherein overcurrent holes are arranged in the water flow direction of the reactor in an up-and-down alternative form and connected with various grid chambers, an anoxic zone grid chamber is arranged at the front end of the reactor, and an aerobic zone grid chamber is arranged at the back end of the reactor; the anoxic zone grid chamber is provided with a stirrer and an agitator blade; the aerobic zone grid chamber is provided with the stirrer, the agitator blade, an aeration riser pipe and an intermediate perforated clapboard; and the aeration riser pipe is internally provided with an aeration head, and sponge filling material is filled below the intermediate perforated clapboard, wherein filling ratio is 30-50%. In the method, shortcut nitrification is achieved above the aerobic zone through low dissolved oxygen (DO is 0.5 <-1>mg/L) and free ammonia (FA) inhibition so that ammonia nitrogen is converted to nitrite nitrogen; and anoxicammoxidation biomembrane acts on the lower part of the aerobic zone, the nitrite nitrogen and ammonia nitrogen are converted to nitrogen, thereby achieving denitrification of autotroph. The method has the advantages of low oxygen consumption, less sludge output and no extra carbon source.