High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H₂) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.