The present invention relates to a wastewater treating system and method for removing pollutants of carbon, nitrogen, phosphorous, comprising: a first reactor contains methanogenic bacteria, PAO and denitrifying bacteria for eliminating the organic carbon in denitrification by denitrifying bacteria, adsorbing partial organic carbon and releasing phosphate by PAO and; metabolizing organic carbon to form methane gas by methanogenic bacteria; a second reactor disposed at the rearward of first reactor, second reactor treats the effluent from first reactor by denitrifying bacteria and PAO, denitrifying bacteria is able to denitrifying the nitrate and PAO is able to process the phosphorous releasing; a third reactor disposed rearward of second reactor, which comprises PAO, heterotrophic bacteria and nitrifying bacteria, wherein PAO is applied for phosphorous accumulating process, the heterotrophic bacteria is applied for carbon removal process, the nitrifying bacteria is applied for nitrifying process; and a membrane separation reactor disposed inside or rear of third reactor to separate various microorganisms and the treated effluent. The present invention applies methanogenic bacteria in the system for decreasing the amount of waste sludge efficiently and reduce power consuming.