Wastewater treatment plants (WWTPs) have been recognized as one of the significant greenhouse gas (GHG) generators, due to the complex biochemical reaction and huge consumption of energy and materials. Recently, WWTPs have been built underground and they will be confronted with the challenges of mitigating GHG emissions and improving the quality of treated wastewater. Here, we focus on estimating GHG emissions to set up effective management plans for a WWTP built underground. First, we apply the process-based life cycle assessment (LCA) with an inventory database of the underground WWTP for a case study. Then, we identify significant factors affecting GHG emissions during service life using sensitivity analysis and suggest the proper tactics that could properly reduce GHG emissions from the WWTP.