Understanding microbial responses to environmental stress is crucial for comprehending their distribution and supporting conservation efforts. Yet, comprehensive evaluations of these responses across diverse microbial taxa within the framework of classical ecological theories are scarce. This gap limits our ability to predict the impact of environmental changes on the diversity and functions of soil microbes in natural settings. In this study, we conducted a field survey across twenty alpine wetlands on the Tibetan Plateau. Employing amplicon sequencing with network theories, we investigated the biodiversity and coexistence of bacteria and archaea under a wide range of natural salinity conditions. Our results demonstrated a linear decrease in bacterial diversity with increased salinity, while archaeal diversity showed a non-linear pattern, initially declining and then rising, reflecting varied adaptation strategies to salt stress. Network analysis revealed a heightened complexity in positive associations among bacteria under salt stress. In contrast, archaea exhibited a decrease in both positive and negative associations, with the community succession to halophiles. These results imply that bacteria may counteract stress through enhanced facilitation, whereas archaea predominantly rely on stress-tolerant taxa. Additionally, structural equation modeling confirmed our hypothesis regarding the ecological response strategies of bacteria and archaea to salinity stress, showing that the variation in bacterial diversity is mainly explained by the complexity of positive associations, whereas archaeal diversity directly correlates with salinity levels. Overall, this study offers novel insights into the ecological strategies of prokaryotes under salinity stress and enriches our understanding of the processes maintaining microbial diversity in stressful conditions.