Orofacial muscles are particularly prone to refractory fibrosis after injury, leading to a negative effect on the patient's quality of life and limited therapeutic options. Gaining insights into innate inflammatory response-fibrogenesis homeostasis can aid in the development of new therapeutic strategies for muscle fibrosis. In this study, the crucial role of macrophages is identified in the regulation of orofacial muscle fibrogenesis after injury. Hypothesizing that orchestrating macrophage polarization and functions will be beneficial for fibrosis treatment, nanomaterials are engineered with polyethylenimine functionalization to regulate the macrophage phenotype by capturing negatively charged cell-free nucleic acids (cfNAs). This cationic nanomaterial reduces macrophage-related inflammation in vitr and demonstrates excellent efficacy in preventing orofacial muscle fibrosis in vivo. Single-cell RNA sequencing reveals that the cationic nanomaterial reduces the proportion of profibrotic Gal3(+) macrophages through the cfNA-mediated TLR7/9-NF-κB signaling pathway, resulting in a shift in profibrotic fibro-adipogenic progenitors (FAPs) from the matrix-producing Fabp4(+) subcluster to the matrix-degrading Igf1(+) subcluster. The study highlights a strategy to target innate inflammatory response-fibrogenesis homeostasis and suggests that cationic nanomaterials can be exploited for treating refractory fibrosis.