It is essential to reduce carbon emissions in wastewater treatment plants (WWTPs) to achieve carbon neutrality in society. However, current optimization of WWTPs prioritizes the operation cost index (OCI) and effluent quality index (EQI) over greenhouse gas (GHG) emissions. This study aims to conduct a multi-objective optimization of a WWTP, considering GHG emissions, EQI, and OCI. The anaerobic-anoxic-oxic integrated membrane bioreactor (AAO-MBR) process in an actual WWTP was selected as a typical case, tens of thousands of scenarios with combinations of six operational parameters (dissolved oxygen (DO), external carbon resource (ECR), poly aluminum chloride (PAC), internal reflux ratio (IRR), external reflux ratio (ERR), and sludge discharge (SD)) were simulated by GPS-X software (Hydromantics 8.0.1). It was shown that ECR has the greatest impact on optimization objectives. In the optimal scenario, the main parameters of ATDO, MTDO, IRR, and ERR were 0.1 mg/L, 4 mg/L, 50%, and 100%, respectively. The EQI, OCI, and GHG of the best scenario were 0.046 kg/m3, 0.27 ¥/m3, and 0.51 kgCO2/m3, which were 2.1%, 72.2%, and 34.6% better than the current situation of the case WWTP, respectively. This study provides an effective method for realizing low-carbon and economical operation of WWTPs.