Abstract: To meet the increasing demand for low-carbon and high-efficiency nitrogen removal in municipal wastewater treatment plants (WWTPs), this study developed a coupled system integrating partial denitrification and anaerobic ammonium oxidation (PD-anammox). The system's nitrogen removal performance was systematically investigated for the simultaneous treatment of municipal wastewater and secondary effluent. In addition, the characteristics of nitrous oxide (N₂O) emissions were evaluated, and reverse transcription quantitative real-time PCR (RT-qPCR) was employed to assess the activity of key functional genes involved in N₂O production and reduction pathways. The coupled system was operated under two different volumetric ratios of municipal wastewater to secondary effluent (1:5 and 2:5). Results demonstrated that, under both operating conditions, the total nitrogen concentration in the effluent consistently remained below 8 mg/L, meeting the stringent discharge standards of WWTPs. The system achieved an average nitrogen removal efficiency exceeding 69%. Notably, the contribution of the anammox pathway to overall nitrogen removal ranged from 69.52% to 75.12%, indicating a reduced dependency on external organic carbon and oxygen. Microbial community analysis using high-throughput sequencing revealed that increasing the proportion of municipal wastewater introduced more complex carbon sources, which significantly reduced the relative abundance of the genus Thauera, a key microorganism associated with partial denitrification. In contrast, the genus Denitratisoma, comprising potential functional bacteria capable of metabolizing diverse carbon compounds, maintained or even enhanced its relative abundance. This suggests its crucial role in supplying stable nitrite to anammox bacteria and thereby contributing to the overall resilience and stability of the system. A particularly noteworthy finding was the substantial reduction in N₂O emission factors at higher proportions of municipal wastewater. This reduction was primarily attributed to decreased dissolved N₂O concentrations rather than increased gas stripping. To further elucidate the underlying mechanisms, RT-qPCR was conducted to quantify the expression of key genes related to N₂O production and reduction. The results indicated that a higher municipal wastewater ratio significantly upregulated both the quinol-oxidizing NO reductase gene qnorB (by 2.47-fold) and the clade Ⅱ N₂O reductase gene nosZⅡ (by approximately 9-fold). Unlike the conventional nosZⅠ, nosZⅡ is commonly found in atypical denitrifying bacteria and exhibits a higher substrate affinity for N₂O, enabling the efficient reduction of dissolved N₂O even at low concentrations. This gene expression pattern explains the observed suppression of N₂O accumulation, as enhanced nosZⅡ activity reinforces the final step of denitrification, converting N₂O to N₂. Overall, this study demonstrates the PD-Anammox coupled system as an effective and sustainable approach for the concurrent treatment of municipal wastewater and secondary effluent, offering high nitrogen removal efficiency with minimized greenhouse gas emissions. By leveraging the functional flexibility of Denitratisoma and the high-affinity N₂O reduction capacity of nosZⅡ-harboring bacteria, the system achieves a synergistic balance between nitrogen removal and climate impact mitigation. These findings provide a novel technical pathway for simultaneously achieving high-efficiency nitrogen removal and N₂O mitigation in biological wastewater treatment.