Solid-state fermentation of Chinese traditional cereal vinegar is a complex and retractable ecosystem with multi-species involved, including few abundant and many non-abundant species. However, the roles of non-abundant species in vinegar fermentation remain unknown. Here, we studied the assembly and co-occurrence patterns for abundant and non-abundant bacterial sub-communities using Zhenjiang aromatic vinegar fermentation as a model system. Our results showed that the change of reducing sugar and total titratable acid were the main driving forces for the assembly of abundant and non-abundant sub-communities, respectively. The non-abundant sub-community was more sensitive to the environmental variation of acetic acid fermentation (AAF) process. Integrated co-occurrence network revealed that non-abundant sub-communities occupied most of the nodes in the network, which play fundamental roles in network stability. Importantly, non-abundant species-Komagataeibacter europaeus, showed the highest value of degree in the co-occurrence network, implying its importance for the metabolic function and resilience of the microbial community. Bioaugmentation of K. europaeus JNP1 verified that it can effectively modulate bacterial composition and improve the robustness of co-occurrence network in situ, accompanied by (i) increased acetic acid content (14.78%) and decreased reducing sugar content (40.38%); and (ii) increased the gene numbers of phosphogluconate dehydratase (212.24%) and aldehyde dehydrogenase (192.31%). Overall, the results showed that non-abundant bacteria could be used to regulate the desired metabolic function of the community, and might play an important ecological significance in traditional fermented foods.