Abstract <p>Ammonia-oxidizing archaea (AOA), a group of key drivers in nitrification, are commonly found in soil. Nitrogen (N) enrichment and the input of litter affect the form of N and its nitrification. However, the response of AOA to integrated N enrichment and plant litter inputs in desert steppe topsoil remains unclear.&#xa0;A field study was conducted that utilized the plant litter of four dominant species in the desert as a treatment, which was integrated with two N enrichment treatments (0 and 9.2&#xa0;mol·N·m⁻²·yr⁻¹). High-throughput sequencing was used to study the response of <i>AOA-amoA</i> to N enrichment and inputs of plant litter in desert steppe topsoil and its associated microbial mechanisms.&#xa0;The soil AOA were sensitive to enrichment with N, and their abundance decreased from 8.8 × 10^5 to 5.5 × 10^5 copies·g⁻² dry soil following the N treatment. Different types of litter also affected the abundance of <i>AOA-amoA</i>, but there was no significant difference between the treatments. Soil organic carbon, ammonium-N, total phosphorus, total salt, and nitrate–N were significantly related to the structure of AOA communities in the desert steppe. Network and Zi-Pi analyses indicated that the application of N significantly increased the number of key species in the AOA community from 5 to 29 and enhanced the competitiveness of the community relationships; the dominant genus in the key population changed from <i>Thaumarchaeota</i> to <i>Crenarchaeota</i>.&#xa0;N enrichment can significantly reduce the abundance of <i>AOA-amoA</i> by altering the AOA keystone species in the topsoil of a desert steppe.</p>