The excessive application of nitrogen fertilizer aggravated the loss of nitrogen in farmland and exerted detrimental effects on the soil and water environment. Examining the effects of N-(n-Butyl)thiophosphoric triamide (NBPT) and nitrification inhibitor dicyandiamide (DCD) on nitrification and crop yield in wheat-corn double cropping systems would provide valuable insights for improving nitrogen efficiency and ensuring a rational application of inhibitors. A field experiment lasting one and a half years was performed in the winter wheat–summer maize double agroecosystem in North China. The four treatments that were applied included (I) conventional fertilization without inhibitors (CK), (II) conventional fertilization with 0.26 g/m² NBPT (NBPT), (III) conventional fertilization with 1.00 g/m² DCD (DCD), and (IV) conventional fertilization with 0.26 g/m² NBPT and 1.00 g/m² DCD (NBPT + DCD). The results demonstrated that the combined use of NBPT and DCD exerted better effects in reducing NO₃⁻-N leaching. Nitrification could be inhibited for up to 95 days by combining NBPT and DCD, while 21 days by DCD. Ammonia-oxidizing archaea (AOA) (R² = 0.07159, p < 0.01) along with ammonia-oxidizing bacteria (AOB) (R² = 0.09359, p < 0.01), rather than a complete ammonia oxidizer (comammox), were significantly and positively correlated with NO₃⁻-N content, which indicated that the ammoxidation process was mainly regulated by AOA and AOB, instead of comammox in the winter wheat–summer maize double agroecosystem in North China.

Crop rotation systems profoundly influence soil phosphorus (P) dynamics through physicochemical and microbial interactions. The mechanisms regulating P availability under various rotational practices remain poorly understood. This five-year field experiment investigated the effects of four rotation systems (WM: wheat–maize; WP: wheat–peanut; WS: wheat–soybean; MV: maize–hairy vetch) on soil P fractions, phosphatase activities, P-cycling gene abundance, and their interactions with soil properties. The WM rotation substantially reduced soil pH (6.29) while increasing labile P fractions (Ca₂-P) and moderately labile P (Al-P, Fe-P, and Ca₈-P), which was attributed to enhanced acid phosphatase activity. The WP rotation elevated soil pH (8.13) but reduced P availability due to calcium–P immobilization. The MV rotation stimulated microbial P cycling, exhibiting the highest phoD (2.01 × 10⁶ copies g⁻¹) and phnK (33,140 copies g⁻¹) gene abundance, which was linked to green manure-induced microbial activation. Redundancy analysis identified soil pH, total nitrogen, and stoichiometric ratios (C/N and N/P) as key shared drivers of P fractions and enzymatic activity. Partial least squares path modeling (PLS–PM) indicated that crop rotation directly regulated P availability through pH modulation (r = −0.559 ***) and the C/N ratio (r = 0.343 ***) while indirectly regulating P fractions through phosphatase activity. Lower C/N ratios (<10) across all rotation regimes amplified the carbon limitation in the process of P transformation, indicating that exogenous carbon inputs and appropriate stoichiometry in the soil should be optimized. The results of this study inform the selection of suitable crop rotation patterns for sustainable agriculture.