The activated sludge process generates a large amount of excess sludge as a byproduct, which is one of the most serious challenges in biological wastewater treatment. In the present study, the feasibility of 2,4,6-trichlorophenol (TCP) and malonic acid (MA) as metabolic uncouplers to reduce sludge generation in the sequence batch reactor (SBR) for treating organic wastewater for a long period was studied. The results showed that 2 mg/L TCP could reduce sludge generation by about 47%, while chemical oxygen demand (COD) removal efficiency and sludge settlability were not obviously influenced. Although 10 mg/L MA could also reduce excess sludge production by about 30% while slightly affecting COD removal, it seriously deteriorated sludge settlability. Accordingly, TCP is a better uncoupler for sludge reduction for a longer period in the SBR for treating organic wastewater, and MA can only be used as a short-term or transitional uncoupler. Microscopic and 16S ribosomal deoxyribonucleic acid analyses showed that the microbial population of sludge varied when uncouplers were fed to the activated sludge system. Occurrence of large amounts of filament and the disappearance of protozoa may be the main reason for the aggravation of sludge settlability under uncoupled metabolic conditions caused by MA.