In this study, a sequencing batch reactor (SBR) was operated as Anammox and used as parent reactor. Then three SBRs seeded from the parent reactor were adopted for investigating the effect of CuO, ZnO and TiO2 nano-particles (NPs) on nitrogen removal, microbial activity and microbial communities of Anammox. The bioactivities of anaerobic ammonia-oxidizing bacteria (AAOB) after different exposure period were detected by batch experiments. Results showed that NPs performed immediate and durable toxicity on Anammox. The nitrogen removal efficiency decreased to 2.3%, 2.9% and 14.0% from 71%, the Anammox rate decreased to 0.13, 0.16 and 0.75 from 2.76 mg h(-1) g(-1) VSS, and the relative abundance of AAOB decreased to 2.57%, 2.78% and 2.61% from 7.99%, respectively. CuO and ZnO NPs performed similar effect, while CuO NPs led to the most severe toxicity and lowest accumulative effect. TiO2 NPs showed the lowest toxicity but most durable suppression on Anammox process.