This study analyzed the antimicrobial, cytotoxic, and antioxidant properties of Cnidiumofficinale (CO) extracts to confirm their antimicrobial activity toward oral microorganisms. The control group contained 0 μg/mL of CO, and the experimental groups contained 50, 100, 150, and 200 μg/mL of CO. To confirm the antibacterial activity of CO extracts against microorganisms in the oral cavity, an inhibition zone test, a colony-forming unit (CFU) analysis, an optical density (OD) evaluation, and a SEM (scanning electron microscopy) analysis were performed. A cytotoxicity test was also conducted to determine cell viability, and the contents of flavonoids and polyphenols were measured to analyze the extract components. In the control group, the growth inhibition zone increased, while the CFU and OD values decreased (p < 0.05). The SEM analysis confirmed that the number of microorganisms for both the microbes decreased. The cell viability was more than 80% in both the control and experimental groups, excluding the 200 μg/mL sample. The flavonoid and polyphenol contents in the experimental groups showed higher values than those of the control group. Therefore, the CO extract showed considerable antimicrobial activity toward both Streptococcus mutans and Candida albicans, suggesting that it may be used as a natural antimicrobial agent for dental applications.