Marine microorganisms have an inherent advantage in the treatment of saline wastewater due to their halophilic properties. Ammonium assimilation is the most important and common nitrogen conversion pathway in the ocean, which means that it may be a suitable nitrogen removal strategy under high salinity conditions. However, the targeted construction of engineering microbiomes with ammonium assimilation function for nitrogen recovery has not been realized. Here, we constructed four halophilic ammonium assimilation microbiomes from marine microbial community under varying chemical oxygen demand (COD) to nitrogen (COD/N) ratios. The regulation of COD/N ratio on microbial self-assembly was explored at the phenotypic, genetic, and microbial levels. The results of nitrogen balance tests, functional genes abundance and microbial community structure confirmed that the microbiomes regulated by different COD/N ratios all performed obligate ammonium assimilation functions. >93% of ammonium, 90% of TN, 98% of COD, and 82% of phosphorus were simultaneously removed by microbial assimilation under the COD/N ratio of 20. COD/N ratios significantly affected the self-assembly of microbiomes by selectively enriching heterotrophic microorganisms with different preference for organic carbon load. Additionally, the increase of COD/N ratio intensified the competition among species within the microbiome (the proportion of negative connections of microbial network increased from 5.0% to 24.4%), which may enhance the stability of community structure. Taken together, these findings can provide theoretical guidance for the construction and optimization of engineering microbiomes for synergistic nitrogen removal and recovery.