<p>The denitrification efficiency of tidal flow constructed wetlands (TFCWs) often limited by the inherently low carbon-to-nitrogen ratio (C/N) of rural domestic sewage (RDS). To address this issue, this study investigated pollutant removal efficiency and greenhouse gas (GHG) emissions in TFCWs enhanced with pyrite, while optimizing key operational parameters including influent mode, operation period, flooding-to-drainage ratio (FDR), and drainage volume. Results demonstrated that the top-inflow TFCWs with pyrite addition significantly enhanced nitrogen removal and reduced GHG emissions. Under optimal conditions (top-inflow, operation period of 12&#xa0;h, FDR of 2:1, and complete drainage), the removal efficiencies of COD, NH₄⁺-N, and TN were 83.76 ± 6.4%, 61.3 ± 10.0%, and 66.4 ± 6.7%, respectively, while N₂O and CH₄ fluxes were 2.0 ± 0.1 and 0.2 ± 0.02&#xa0;mg/(m²·h). Characterization of pyrite revealed a reduction in FeS₂ peaks and the appearance of N1s peaks after the experiments, indicating its active participation in nitrogen removal. Moreover, the surface contents of Fe₂O₃ and SO₄²⁻ increased by 28.8–30.1% and 26.6–55.1%, respectively, confirming redox transformations during the process. Microbial community analysis showed that although the top five genera exhibited similar total relative abundances under different drainage conditions (34.5% and 34.3%), their compositions differed substantially, suggesting that drainage volume influenced system performance by altering microbial structure. Furthermore, under full drainage, pyrite-amended, top-inflow TFCWs exhibited 1.3–7.7% higher relative abundances of dominant denitrifying genera (e.g., <i>Dechloromonas</i>, <i>Pseudarthrobacter</i>, and <i>Zoogloea</i>) demonstrating enhanced denitrification capacity. This study provides novel insights into optimizing TFCWs for efficient treatment of low C/N RDS with simultaneous mitigation of GHG emissions.</p> Graphical abstract <p></p>