Candida albicans and Staphylococcus aureus specifically often resulted in biofilm-associated diseases, ranging from superficial mucosal to life-threatening systemic infections. Recent studies reported that chelerythrine displayed antimicrobial activities against a few microorganisms, but its effects on mono- and dual-species biofilms of C. albicans and S. aureus have never been reported. The purpose of this study was to evaluate the efficacy of chelerythrine against mono- and dual-species biofilms, and explore its effect on the hyphal growth and the hypha-to-yeast transition of C. albicans. The results showed that minimum inhibitory concentrations (MICs) and minimum biofilm inhibitory concentration (MBIC90S) of chelerythrine against planktonic cells of mono-species were 4 and 2 μg/mL, while the MIC and MBIC90 were 6 and 3 μg/mL for dual-species. Meanwhile, the decrease in three matrix component levels and tolerance to antibiotics of biofilms formed by mono- and dual-species exposed to chelerythrine were confirmed by a confocal laser scanning microscope, in conjugation with five fluorescent dyes and a gatifloxacin diffusion assay. Moreover, C. albicans and S. aureus mono-species showed a 96.4, and 92.3% reduction, respectively, in 24-h preformed biofilm biomass in the presence of 128 µg/mL of chelerythrine. Similarly, preformed (24 h) dual-species biofilm biomass also displayed a significant reduction (90.7%) when treated with 192 μg/mL chelerythrine. Chelerythrine inhibited hyphae formation of C. albicans at 4 μg/mL, and C. albicans in hypha-form can be converted into yeast-form at 8 μg/mL of chelerythrine. Therefore, chelerythrine shows promise as a potential antimicrobial and antibiofilm agent for clinical effective treatments of mono- and mixed-species and/or biofilm-associated infections.