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Microbial co-occurrence is a ubiquitous ecological phenomenon, yet we know surprisingly little of the relative importance of bacteria, fungi, and archaea for structuring their co-occurrence network, especially in natural ecosystems. Here, we present a visualization of the soil microbial co-occurrence network pattern based on a sampling from across the eastern Tibetan Plateau. We found more intra-kingdom than inter-kingdom links within the network, and most of these links were positive. Compared with module hubs and network hubs, the connectors had more connections with environmental variables, and among the microbial groups the archaea built more connections than did bacteria or fungi, which pointed to the greater ecological importance of the archaea in constructing the overall network. Omitting the archaea resulted in a lower natural connectivity, suggesting this group is crucial for enhancing the robustness of the microbial co-occurrence network. Taken together, our results suggest that the archaea play a critical role in constructing soil microbial co-occurrence networks in the Tibetan plateau, and possibly also in other similar climate change-sensitive regions.