Objectives <p>To reveal the cellular composition and molecular environment of the inflammatory infiltrates in residual deep pockets of severe periodontitis following non-surgical periodontal therapy (NSPT). This may provide critical insights for targeted therapy in managing severe periodontitis.</p> Methods <p>Single-cell RNA-seq (scRNA-seq) and bulk RNA-seq of periodontal tissues from patients with severe periodontitis following NSPT and healthy donors were performed. Eligible public datasets of scRNA-seq and bulk RNA-seq were also used for analysis. Multiplex immunohistochemical immunofluorescence was used to validate the identified cell subtypes further.</p> Results <p>We identified a diverse inflammatory microenvironment landscape in the residual deep pockets of severe periodontitis after NSPT, in which IL-6⁺ fibroblasts were enriched in the deep pocket granulation tissue of severe periodontitis. The hypoxic microenvironment orchestrated by IL-6⁺ fibroblasts was closely associated with the persistent inflammation in severe periodontitis after NSPT. The infiltration of IL-6⁺ fibroblasts and FCN1⁺ macrophages exhibited a strong correlation, suggesting a potential crosstalk between the two cell subtypes. The coexistence of IL-6⁺ fibroblasts and FCN1⁺ macrophages was associated with sustained inflammatory responses, response to hypoxia and oxidative stress, osteoclast differentiation, and bone resorption in severe periodontitis after NSPT.</p> Conclusions <p>Our study unveiled the presence of a fibroblast-mediated network localized in the hypoxic region of the severe periodontitis that functionally linked macrophages and fibroblasts, which collaborate to exacerbate the periodontal inflammation microenvironment. These findings may offer a new perspective for the targeted treatment of severe periodontitis, especially the targeted treatment against IL-6⁺ fibroblasts.</p>