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Biochar has been widely recognized as an effective and eco-friendly ameliorant for saline soils, but information about the mechanism of how biochar influences nitrification in salt-affected agroecosystem remains fragmented. An incubation experiment was performed on the salt-affected soil collected from a three-consecutive-year experiment at biochar application gradients of 7.5 t⋅ha⁻¹, 15 t⋅ha⁻¹ and 30⋅t ha⁻¹ and under nitrogen (N) fertilization. Responses of the nitrification rate (NR), numbers of ammonia monooxygenase (<i>amoA</i>) gene copies, and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to biochar application were investigated. The results indicated that, under N fertilization, the NR and numbers of <i>amoA</i>-AOB and <i>amoA</i>-AOA gene copies negatively responded to biochar addition. Biochar application increased the community diversity of AOB but decreased that of AOA. Biochar addition and N fertilization shifted the AOB community from <i>Nitrosospira</i>-dominated to <i>Nitrosospira</i> and <i>Nitrosomonas-dominated</i>, and altered the AOA community from <i>Nitrososphaera</i>-dominated to <i>Nitrososphaera</i> and <i>Nitrosopumilus</i>-dominated. The relative abundance of <i>Nitrosospira</i>, <i>Nitrosomonas</i> and <i>Nitrosopumilus</i> decreased, and that of <i>Nitrosovibrio</i> and <i>Nitrososphaera</i> increased with biochar application rate. Soil SOC, pH and NO₃⁻-N explained 87.1% of the variation in the AOB community, and 78.1% of the variation in the AOA community was explanatory by soil pH and SOC. The SOC and NO₃⁻-N influenced NR through <i>Nitrosovibrio</i>, <i>Nitrosomonas</i>, <i>Norank_c_environmental_samples_p_Crenarchaeota</i> and <i>amoA</i>-AOB and <i>amoA</i>-AOA gene abundance. Therefore, biochar addition inhibited nitrification in salt-affected irrigation-silting soil by shifting the community structures of AOB and AOA and reducing the relative abundance of dominant functional ammonia-oxidizers, such as <i>Nitrosospira</i>, <i>Nitrosomonas</i> and <i>Nitrosopumilus</i>.