Objective This study was carried out to evaluate the response of paddy soil anammox bacterial activity, abundance and community structure to rice straw returning and different tillage practices.Method Three different till treatments (conventional till, rotary till and no-till) + rice straw returning were set up, with conventional till and no rice straw returning as control. The potential activity, functional gene (hzsB) abundance and community structure of anammox bacteria were analyzed by ¹⁵N tracing, fluorescent quantitative PCR and Illumina sequencing, respectively.Result Anammox activity showed a significant difference and the values ranked as no-till > rotary till > conventional till(P < 0.05), while no significant difference was observed between control and rotary tillage+rice straw. Also, no significant difference was detected in the copy number of hzsB among treatments. Two known anammox bacteria (Kuenenia and Scalindua) and some unidentified genera were identified by Illumina sequencing, and the relative abundance of Kuenenia and Scalindua showed a negative correlation (P < 0.05). Pearson correlation analysis showed that anammox activity was significantly correlated with denitrification activity, but not with hzsB abundance and community composition.Conclusion We conclude that anammox activity and community composition but not the functional gene abundance respond to long term straw returning and different tillage practices. Rice straw returning + conventional till in rice field may inhibit N loss to some extent, while rice straw returning + no-tillage increased soil N loss. This study may provide a scientific basis for nitrogen (N) management in paddy fields.