The enhancement of carbon sequestration and emissions reduction has emerged as a primary concern in China’s rural regions. Nevertheless, numerous completed rural wastewater treatment facilities necessitate retrofitting due to suboptimal operational conditions. Consequently, evaluating the greenhouse gas (GHG) emissions impact and carbon reduction advantages of rural wastewater treatment facility retrofitting is essential. Existing research predominantly focuses on urban wastewater treatment plants, with minimal attention given to GHG emissions impact during the construction and demolition stages of wastewater treatment facilities. In this investigation, we developed a life cycle assessment (LCA)-based evaluation model to appraise the GHG emissions impact and carbon reduction benefits of retrofitting rural wastewater treatment facilities. We examined a renovation project in Sanxiushan Village, Xiamen City, Fujian Province, incorporating the integrated plant treatment technology of constructed wetlands. Our findings indicate that retrofitting offers significant advantages in terms of GHG emissions reduction, even when accounting for implicit GHG emissions. The establishment of supplementary terraced constructed wetlands and landscape greening can yield more substantial carbon reduction benefits. Moreover, we discovered that implicit GHG emissions during the construction stage can be mitigated by employing local, recycled, and low-carbon materials. Modifying vegetation community structure and prioritizing vegetation species selection can enhance the carbon storage capacity of plants, reducing overall life cycle GHG emissions and augmenting emissions reduction benefits. The evaluation model developed in this study can facilitate the promotion of low-carbon construction and operation of rural wastewater treatment facilities.