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The use of nitrification inhibitors has been suggested as a strategy to decrease cadmium (Cd) accumulation in crops. However, the most efficient nitrification inhibitor for mitigating crop Cd accumulation remains to be elucidated, and whether and how changes in soil microbial structure are involved in this process also remains unclear. To address these questions, this study applied three commercial nitrification inhibitors, namely, dicyandiamide (DCD), 3,4-dimethylpyrazole phosphate (DMPP), and nitrapyrin (NP), to pakchoi. The results showed that both DCD and DMPP (but not NP) could efficiently decrease Cd concentrations in pakchoi in urea- and ammonium-fertilized soils. In addition, among the three tested nitrification inhibitors, DMPP was the most efficient in decreasing the Cd concentration in pakchoi. The nitrification inhibitors decreased pakchoi Cd concentrations by suppressing acidification-induced Cd availability and reshaping the soil microbial structure; the most effective nitrification inhibitor was DMPP. Ammonia oxidation generates the most protons during nitrification and is inhibited by nitrification inhibitors. Changes in environmental factors and predatory bacterial abundance caused by the nitrification inhibitors changed the soil microbial structure and increased the potential participants in plant Cd accumulation. In summary, our study identified DMPP as the most efficient nitrification inhibitor for mitigating crop Cd contamination and observed that the soil microbial structural changes caused by the nitrification inhibitors contributed to decreasing Cd concentration in pakchoi.