Abstract The nitrification, which utilized ammonium nitrogen (NH 4 + ‐N) as substrate, is susceptible to the bioavailability of NH 4 + ‐N. However, it is unclear how the nitrification process responds to the decrease of NH 4 + ‐N availability due to nanoattipulgite (NA) addition, especially in salt‐affected soils. A pot experiment was performed to study the effect of different NA rates (NA0, NA1, and NA2: 0, 25, 50 g kg −1 ) and nitrogen fertilizer (F) gradients (F1, F2, and F3: 54, 81, 108 mg N kg −1 ) on the net nitrification rate (NNR), abundance of ammonia monooxygenase ( amoA ) gene copies, and communities of ammonia‐oxidizing archaea (AOA) and bacteria (AOB) in a moderately salinized fluvo‐aquic soil. The concentrations of NH 4 + ‐N and nitrate nitrogen in soils showed insignificant differences among various NA treatments. The addition of NA reduced NNR after topdressing but had no significant effect on NNR after base fertilizer. Nitrogen fertilizer could decrease the amoA gene abundance of AOA and increase the amoA gene abundance of AOB in soil. NA could maintain the relative stability of AOB amoA gene abundance. NA treatment only changed the community composition of AOB before topdressing at the F2 level but did not change the community composition of ammonia‐oxidizing microorganisms under other conditions. Overall, NA adsorbs more NH 4 + ‐N and indirectly affects nitrification by reducing the stimulating effect of F on the activity of ammonia‐oxidizing microorganisms, which can play an important role in reducing nitrate pollution and denitrification loss from saline soil.