Objective To identify the strain CC-3 isolated and purified from the facial skin lesions of an acne patient, and to explore the traditional Chinese medicine (TCM) formulas. Methods The phylogenetic relationship of strain CC-3 was determined biochemical identification by VITEK-2 fully automatic bacterial identification system and morphological characteristics, and phylogenetic tree based on 16S rDNA sequence. The minimum inhibitory concentration(MIC) of the CC-3 was determined by 96-well plate method, and the effect of TCM on acne was analyzed by the minimum inhibitory concentration. Results The strain CC-3 was identified as C. acnes CC-3, based on biochemical analysis of the VITEK 2 fully automatedly bacterial identification system and the morphological characteristics and 16S rDNA sequence alignment. Both formula one and formula two of TCM inhibited C. acnes CC-3 in vitro, and the minimum inhibitory concentrations of formulaone and formula two were seperatedly 0.01 g/mL and 0.63 g/mL. Conclusion The strain CC-3 was identified as C. acnes CC-3. Both formula one and formula two had in vitro inhibitory effects on C. acnes CC-3, and the inhibitory effect of formula one was better than that of formula two.