Chinese medicine herbal extracts are ideal candidates to replace toxic industrial wood preservatives thanks to their antifungal and nontoxic properties. To investigate the antifungal activity of Chinese herbal medicines, in this study, Trametes versicolor fungi were selected as test strains to evaluate the antifungal properties of Fructus Cnidii, Fructus Forsythiae, and Radix Stemonae. The results show that Fructus Cnidii has a strong inhibitory effect against T. versicolor, whereas Fructus Forsythiae and Radix Stemonae have a weak inhibitory effect. The hyphae growth cycle shows that the three studied Chinese herbs disrupt the growth of T. versicolor. Moreover, instead of direct killing, the Chinese herbal medicine demonstrated inhibition ability. Furthermore, the morphological and toxicological evidence shows that Fructus Cnidii affected the expression of proteins or enzymes to achieve the inhibition goal. In sum, this study could provide both primary data and a theoretical foundation for further developing and applying for traditional Chinese medicine as a green type of wood preservative.