Background and Aims <p>The addition of a nitrification inhibitor (NI) lowers soil CO₂ emissions, but the potential source of soil CO₂ emissions reduction remains unclear.</p> Methods <p>A series of incubation experiments was conducted using three calcareous soils to quantify CO₂ emissions. The contribution partitioning of soil organic carbon (SOC) and inorganic carbon (SIC) to CO₂ fluxes under NI amendment was quantified using stable isotope mixing models. NH₃ and N₂O emissions were simultaneously monitored to analyze the synergistic mechanisms of soil C and N emissions regulation through NI amendment.</p> Results <p>N application stimulated the SIC-derived CO₂ emissions from Beijing, Sichuan, and Kunming soils, contributing 61.4%, 64.8%, and 67.9% of CO₂ emissions, respectively. NI amendment significantly reduced the total soil CO₂ emissions (31.3%, 23.7%, and 11.1%, respectively) and lowered the contribution of SIC to CO₂ emissions (2.9%, 29.4%, and 5.5%, respectively) compared to N treatment. Additionally, NI amendment significantly decreased N₂O emissions from Beijing, Sichuan, and Kunming soils by 57.7%, 81.0%, and 37.3%, respectively, but significantly increased NH₃ volatilization by 26.7%, 39.1%, and 22.8%, respectively, compared to conventional N treatment. Rapid nitrification drove an increase in soil N₂O and CO₂ emissions (high redox potential and nitrate content) but lowered the NH₃ loss.</p> Conclusion <p>This study comprehensively demonstrates the effect of NI on the source of soil CO₂ emissions and the coordinated mechanism of soil CO₂, N₂O, and NH₃ emissions. The findings provide strong evidence for the role of NI in conserving the soil inorganic carbon pool but also underscore the need to address the associated trade-off of increased ammonia (NH₃) loss.</p> Graphical Abstract <p></p>