Conventional filling therapy fails to fundamentally reduce oral cariogenic bacteria. Thus, oral microbiota follow-up intervention after filling would be necessary for improving dental caries prognosis. We recruited 9 caries-free individuals, and 89 dental caries subjects (5 dropouts). Eighty-nine patients were randomized into three groups: caries (n = 8; no treatment), control (n = 40; filling), and postbiotics (n = 41; filling and 14-day Probio-Eco® intervention). Salivary samples were collected at 0 day (after filling) and 14 days. Our results showed that the diversity of dental caries oral microbiota was significantly increased compared with healthy subjects, and filling could restore a healthier oral microbiota partially and temporarily. Thepostbiotics intervention keeps a low alpha-diversity. Co-occurrence network analysis showed that a more stable oral microbiota structure after postbiotics intervention. Taxonomic and functional annotation of the microbiota revealed that postbiotics co-treatment significantly: increased the relative abundance of Pseudomonas and P. reactans, decreased the relative abundance of Prevotella shahii, and enriched the energy metabolism-related pathways. BugBase-predicted phenotypes inferred to an oral microbiota with decreased potential pathogenic bacteria and increased oxidative stress-tolerant bacteria after postbiotics intervention. Collectively, it suggested that postbiotics co-treatment could be a promising strategy that restores the oral microecological balance for dental caries.