The discovery of complete ammonia oxidizers (comammox) challenged our cognition of the nitrification process. Ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and comammox can carry out soil autotrophic nitrification process together. However, the differentiation of the ecological niche of three types of ammonia oxidizers in different environments has not been fully discovered. In this study, a typical black soil collected from northeast China was adjusted to different pH (original and adjusted pH were 4.29 and 7, respectively) and NH₄⁺-N concentrations (weekly adding and without adding 100 mg NH₄⁺-N kg^− 1 soil). The activities of AOA, AOB and comammox were examined using DNA stable isotope probing approach with ¹³CO₂, the phylogenetic information of active ammonia oxidizers was detected by high-throughput sequencing. The results showed that niche differentiation of AOA, AOB and comammox in black soils differed with soil pH. AOA dominated the nitrification process in acidic soils, while AOA, AOB and comammox Clade A taken part in the nitrification process in neutral soils. Among them, AOB showed strong activity in the soils with the high N treatment. The active AOA mainly belonged to Nitrososphaera in acidic and neutral soils. The active AOB and comammox Clade A mainly belonged to Nitrosospira and Clade A.2 in neutral soils, respectively. Taken together, the results highlighted the significance of canonical ammonia oxidizers in nitrification process of black soils, and comammox Clade A played an active role in neutral condition.