The drainage from high fluoride saline-alkali paddy fields exacerbates agricultural non-point source pollution. Constructed wetlands (CWs) have proven effective in treating such drainage, yet most research has focused on the response mechanisms of CWs to either saline-alkali or fluoride stress individually. The impact of combined stress of saline-alkali and fluoride on CW’s purification effects and greenhouse gas emissions, along with the underlying microbial mechanisms, remains unclear. We constructed mesocosm-scale CWs with four treatments varying in influent saline-alkali levels: low (LS-CWs), medium (MS-CWs), high (HS-CWs), and non saline-alkali CWs (Control-CWs). Our results show that CWs were effective in treating low and medium saline-alkali wastewater. Under high saline-alkali condition (pH: 9.5; EC: 5 mS/cm), CWs exhibited the highest global warming potential (GWP), exceeding that of Control-CWs, LS-CWs, and MS-CWs by 2.2, 4.2, and 3.9 times, respectively. The “ infer Community Assembly Mechanisms by Phylogenetic-bin-based null model ” (iCAMP) analysis indicated that stochastic processes, particularly drift and diffusion limitation (DL), dominated the community assembly of CWs. Elevated saline-alkali levels may enhance microbial habitat differentiation, increasing DL’s contribution, and raising the modularity and complexity of co-occurrence networks. This might be a strategy for microbial communities to resist environmental pressure and maintain network stability. We also propose suitable areas for CWs establishment considering both purification efficiency and GWP, in Western Jilin Province, a typical saline-alkali region. This study addresses a research gap in understanding pollutant transformation and microbial response mechanisms during treating saline-alkali and fluoride-laden drainage within CWs, providing a theoretical basis for the integrated treatment of sewage and greenhouse gas control in CWs to maximize their environmental benefits in practical applications.