Landfill leachate treatment processes tend to emit more N2O compared to domestic wastewater treatment. This discrepancy may be ascribed to leachate water characteristics such as high refractory COD, ammonium (NH4+) content, and salinity. In this work, the leachate influent was varied to examine the N2O emission scenarios. NH4+-N, COD, and Cl− concentrations ranged between 1000–2500, 1000–10,000, and 500–3000 mg L−1, respectively. Simultaneously, we attempted to combine statistical analysis with high-throughput sequencing to understand the microbial mechanism with regards to N2O emission. Results show that the strong N2O emissions occur in the nitrifying tank due to the intensive aeration. The system receiving the lowest COD shows the maximum N2O emission factor of 42.7% of the removed nitrogen. Both redundancy analysis and a structural equation model verify that insufficient degradable organics are the key water parameter triggering intensive N2O emission within the designed influent limits. Furthermore, two essential but non-abundant functional bacteria, Flavobacterium (acting as a denitrifier) and Nitrosomonas (acting as a nitrifier), are identified as the core functional species that dramatically influence N2O emissions. An increase in influent COD promotes the proliferation of Flavobacterium and inhibits Nitrosomonas, which in turn reduce N2O release. Meanwhile, two keystone species of Castellaniella and Saprospiraceae unclassified are recognized. They may supply a suitable niche and integrity of the microbial community for N-cycle functional bacteria. These findings reveal the essential role of non-abundant species in microbial community, and expand the current understanding of microbial interactions underlying N2O dynamics in leachate treatment systems.