In biological wastewater treatment, salinity can significantly restrict bacterial activity, and a long adaptation period to the saline condition is needed. This study investigated the feasibility of using partial nitritation-anammox (PNA) in an integrated fixed-film activated sludge (IFAS) reactor for enhanced biological nitrogen removal from saline municipal wastewater. The experimental results show that the salinity increase in the influent seriously affected the activity of anammox bacteria and disrupted the PNA process for autotrophic nitrogen removal when seawater was added to a 20% proportion with a resultant salinity of around 6.5‰. However, the addition of N2H4 (dosage: 5 mg/L for 3 weeks), an exogenous enhancer of both ammonia-oxidizing bacteria and anammox bacteria, effectively facilitated the rapid recovery and adaptation of PNA to salinity stress with a negligible additional cost for long-term operation. The PNA-IFAS reactor achieved a nitrogen removal capacity of 83.4 ± 5.9 mg N/(L‧d) in treating the saline municipal wastewater containing 40% seawater and an ammonia-N concentration of around 60 mg N/L. Salinity in the influent advantageously suppressed the activity and growth of the co-existing nitrite-oxidizing bacteria (NOB). The relative abundances of NOB in the suspended sludge (0.15%) and biofilms (0.33%) were kept at low levels, maintaining a low nitrate yield of 6.6 ± 1.5% in the bioreactor. The result suggests that salinity in the influent may offer potential benefits for reducing the risk of nitrate build-up and increasing the robustness of the PNA process for sustainable wastewater treatment.