The invention discloses an automatic treatment system and an automatic treatment method for removing nitrogen and phosphorus from wastewater. The automatic treatment system comprises a sewage treatment system and an automatic control system, wherein the automatic control system comprises a monitoring device and a remote control device; the sewage treatment system comprises an anaerobic tank, a facultative tank and an aerobic sludge tank, wherein a water distribution guide wall is arranged between the facultative tank and the aerobic sludge tank, the anaerobic tank is internally provided with a submersible stirrer, the facultative tank is internally provided with an inverted-umbrella-shaped surface aerator, the aerobic sludge tank is internally provided with a low-speed mixing flow booster, a water decanter, a submersible nitrification return pump and a sludge-discharge submersible pump and meanwhile, the aerobic sludge tank is externally connected with a frequency conversion fan and a liquid caustic soda adding pump. By introducing the automatic treatment system, the labor intensity is decreased, the wastewater treatment work is smarter and the overall operating cost is reduced. In addition, by adopting the automatic treatment method, namely, intermittent service of the anaerobic tank and the facultative tank according to the drainage requirement of the aerobic sludge tank, the purposes of individual and flexible running and in-series running are achieved and the phosphorus and nitrogen removal effect is greatly improved.