The ectopic fermentation system (EFS) is an advanced technology for treating farm wastewater, and it reduces ammonia nitrogen emission and nitrogen loss of fermentation products. This study observed the functional bacteria succession related to nitrogen metabolism in EFS by high throughput sequencing, and evaluated their associations with environmental factors. Results revealed that with the changes of temperature, pH, moisture content, and nitrogen content during fermentation, the species richness and diversity of ammonia oxidizing bacteria (AOB) with amoA increased, but those of denitrifying bacteria carrying nirK and nosZ decreased. During the fermentation process, the dominant bacterial populations of AOB and denitrifying bacteria changed significantly, and different bacterial populations showed different positive/negative correlations with the environmental factors. This study revealed the role of functional bacteria in ammonia removal and nitrogen conservation of EFS, and provided a theoretical basis for the improvement of microbial agents and EFS application.