Objectives In order to improve the water solubility and antibacterial activity of the low water-soluble antifungal drug ketoconazole (KCZ) and reduce the limits of clinical application. Methods The inclusion complex of ketoconazole-methyl-β-cyclodextrin was prepared with the saturated solution method. The water solubility of the inclusion complex was measured with high-performance liquid chromatography (HPLC). Fourier transform infrared spectroscopy (IR) was used to characterize the structure of the inclusion complex. The in vitro antibacterial activity of the single ketoconazole and the inclusion complex of ketoconazole-methyl-β-cyclodextrin against Candida albicin was comparatively tested with method of sheet diffusion (K-B) and minimum inhibitory concentration (MIC). Results The water solubility of ketoconazole in the inclusion complex was about 2 941 times higher than that of single ketoconazole through the inclusion of methyl-β-cyclodextrin. The formation of new phases was confirmed by Fourier transform infrared spectroscopy (IR). The antibacterial zone of single ketoconazole and the inclusion complex was (22.00±1.63) mm and (28.00±1.63) mm. The minimum inhibitory concentration (MIC) of single ketoconazole and the inclusion complex was (0.125±0.029) μg/mL and (0.062 5±0.015 0) μg/mL. Conclusions The inclusion complex of ketoconazole methyl-β-cyclodextrin did not destroy the original antibacterial ability of ketoconazole against Candida albicans, but improved its antibacterial effect.