This study investigated the antimicrobial potential of Coptis chinensis rhizome extract against key oral pathogens and evaluated the safety and clinical efficacy of a CCE-loaded mouthwash. CCE exhibited broad-spectrum bactericidal activity, with low minimum inhibitory concentrations (0.002–0.008%) and minimum bactericidal concentrations (0.004–0.016%) against Streptococcus mutans, Aggregatibacter actinomycetemcomitans, and Porphyromonas gingivalis. Time-kill kinetics revealed that CCE promptly eradicated Porphyromonas gingivalis. To balance antimicrobial potency and sensory acceptability, specifically the extract’s bitterness, we established the CCE concentrations in the mouthwash at 0.01% and 0.02% (w/v). Preclinical safety evaluations in animal models, including oral mucosal irritation and skin sensitization tests, confirmed the biocompatibility of 0.02% CCE, yielding “None” and “Non-sensitizer” ratings, respectively. Furthermore, a four-week, randomized, double-blind clinical trial (n = 73) revealed that 0.02% CCE mouthwash substantially reduced halitosis-inducing volatile sulfur compounds (hydrogen sulfide by 59.5% and methyl mercaptan by 50.0%). Significant improvements were also observed in the Plaque Index (55.2% reduction), Gingival Index (52.0% reduction), and Bleeding on Probing (77.3% reduction), with no adverse effects. These findings provide preliminary evidence that CCE mouthwash improves halitosis-related parameters and gingival indices in adults with self-reported halitosis, though further research is required to evaluate its long-term impact on broader periodontal disease states.