Periodontitis is a chronic infection where abnormal host‐microbiota interactions alter the oral microbiome, trigger a proinflammatory immune response, and cause inflammatory alveolar bone loss. While antibiotics are occasionally necessary for treating periodontitis, their use must be carefully managed to prevent the development of drug resistance and oral dysbiosis. Therefore, it's crucial to develop new treatment strategies for periodontitis that reduce antibiotic dependence while effectively controlling the inflammation triggered by bacteria. In this study, a hydrogel is engineered by grafting cationic polyamidoamine dendrimers (PAMAM‐G3) onto the oxidized carboxymethyl cellulose (OCMC) backbone, resulting in an injectable cationic hydrogel (OCMC‐PAMAM‐G3, O‐P). This hydrogel can capture anionic microbial‐associated molecular patterns (MAMPs), such as lipopolysaccharides (LPS) and cell‐free DNA (cfDNA). These findings reveal that using O‐P application circumvents the disruption of the oral mucosa microbiome caused by traditional antibiotics. Additionally, this hydrogel can mitigate inflammatory alveolar bone loss in a ligature‐induced periodontitis mouse model by alleviating the LPS/cfDNA‐TLR4/9 pathway. Moreover, topical administration of O‐P hydrogel has no significant adverse effects on the oral mucosa microbiome while improving the local subgingival microbiome. The study highlights a strategy targeting MAMPs while avoiding antibiotics, as it can mitigate the bacteria‐triggered proinflammatory immune response and potentially preserve oral dysbiosis.