Nitrite-oxidizing bacteria (NOB) have been recognized as important members for nitrogen cycling in agricultural ecosystems, and how NOB respond to long-term fertilization and variations at soil aggregate levels remain unclear. In this study, the potential nitrite oxidation activity(PNO) and the abundance of nitrite oxidizers were examined in three aggregate fractions (2000-250, 250-53, <53 μm) of a Black soil under four fertilization regimes. Pyrosequencing was utilized to characterize the composition and distribution of Nitrobacter- and Nitrospira-like NOB populations. PNO was higher in microaggregates (250-53μm) and lowest in silt+clay fraction (<53μm). Fertilization affected PNO to a higher extent than the aggregate sizes. The maximum abundances of Nitrobacter and Nitrospira were observed in macroaggregates (2000-250μm), followed by microaggregates and silt+clay. Dominant (relative abundance >1%) Nitrobacter OTUs were phylogenetically related to some known groups of Nitrobacter environmental clones and those of Nitrospira were affiliated with the Namibia soil cluster, Nitrospira lineage II and V, and Unknown affiliation. Multi-response permutation procedures analysis indicated that nitrifier community was strongly affected by the fertilized regimes but that the aggregate effects were only detectable in the unfertilized soils. Redundancy analysis showed that the community composition of Nitrobacter- and Nitrospira-like NOB was affected by soil total phosphorus, available phosphorus, total potassium and NH₄⁺ content. Our findings suggest that fertilization treatments rather than soil aggregates play more important roles in shaping NOB community structure.