By constructing feature metagenome database of complete ammonia oxidizing bacteria (CAOB), their abundance and diversity in 56water treatment systems, e.g., urban wastewater nitrogen systems and drinking water treatment systems, were quantitatively analysed. The significant influencing factors were determined by statistical analysis and the influential mechanism were analysed. It was revealed that CAOB were accounted for 8.2%~99.6% of the ammonia oxidation community and 1.4%~48.6% of the Nitrospira in the surveyed urban wastewater nitrogen removal systems. Phylogenetic analysis revealed that CAOB metagenome assembled genomes (MAGs) were associated with Ca.Nitrospira nitrosa, with ANI value higher than 94%. CAOB community were more homogeneity than those in drinking water treatment systems, speculating that Ca.Nitrospira nitrosa cluster were specific adaptable to urban wastewater nitrogen removal systems. According to correlation analysis, pH value was significantly positively while COD was significantly negatively correlated with the abundance and diversity of CAOB. They were more likely to be dominant nitrifiers in low NH₄⁺, high sludge retention time, and low dissolved oxygen conditions. In conclusion, this study reveals that Ca.Nitrospira nitrosa cluster are dominant CAOB, and their distribution influencing factors in urban wastewater nitrogen removal systems.