Aiming at the problems of high ammonia nitrogen bio-toxicity, complex process, high cost and poor nitrogen removal in the currently available process for the treatment of raw swine wastewater from intensive livestock farms, a three-dimensional structure rotating biological contactor (3D-RBC) using heterotrophic nitrification-aerobic denitrification (HN-AD) functional bacteria as the microbial inoculants, was proposed for the treatment of raw swine wastewater. The rapid biofilm culturing in the 3D-RBC reactor was achieved in only 15days by using HN-AD bacteria agent as the microbial inoculants. By controlling linear velocity of the rotating disc and changing the influent C/N, the enrichment of the dominant HN-AD bacteria in the reactor and the start-up of the pretreatment process were completed in 65days. The raw swine wastewater was then treated by this process. Due to the strong tolerance of high ammonia nitrogen of the HN-AD bacteria, the removal efficiency of COD, NH₄⁺-N and TN was 69.8%, 87.9% and 79.5%, respectively, indicating significant reduction of the pollutants in the raw wastewater. The high-throughput sequencing technology was used to study the changes of microbial community structure during the superiority construction process of the functional bacteria. The results showed that, the dominant HN-AD bacteria within the biofilm gradually changed from Halomonas and Acinetobacter to Comamonas and Hydrogenophaga, and the relative abundance of which increases obviously. The SEM results further confirmed the enrichment of functional microorganisms, the biofilm uses Filamentous bacteria as the skeleton and the surface of the biofilm layer tightly attached to the filler was enriched in rod-like and globular bacteria, which was in consistent with the results of the biodiversity analysis.