Display omitted •Manure application significantly increased both PAO and PNO.•Manure fertilization augmented nitrifier abundance.•Soil NH4+-N and TC are good indicators for NOB and comammox community.•Community composition of NOB and comammox was affected by both soil type and manure fertilizer.•Manure fertilizer made nitrifier community more closely linked and stimulated the function performance of nitrifiers. Nitrification plays an important role in the soil nitrogen cycle. Here, we conducted an experiment in three different soil types (red soil, black soil, and alluvial soil) to evaluate the response of nitrifiers and nitrification to manure fertilizers. We found that long-term manure fertilization altered the soil physicochemical properties, increased soil organic matter and NO3－-N concentrations, and decreased NH4+-N concentrations. Both ammonia and nitrite oxidation potential were higher in the manured soils than those in the control soils. Long-term manure fertilization markedely increased the abundance of nitrifiers and the abundance of the complete ammonia oxidation (comammox) amoA gene copy number ranged from 0.78 × 106 to 2.18 × 106 g−1 dry soil, which was lower than that of canonical nitrifiers including ammonia‐oxidizing archaea, ammonia‐oxidizing bacteria, and nitrite‐oxidizing bacteria (NOB). The community composition of NOB and comammox was affected by both soil type and manure fertilizer. Soil NH4+-N concentration and total carbon content were the factors that were most strongly correlated with the microbial community composition. Manure fertilizers promoted the coupling linkages among soil Nitrobacter, Nitrospira, and comammox communities and created a more closely linked microbial community. The results suggest that long-term inputs of manure to agricultural soils influence the structure of NOB and increase nitrification rates.