The optimal combinatorial parameters of antimicrobial photodynamic therapy (aPDT) mediated by methylene blue (MB) with the addition of potassium iodide (KI) against Candida species have never been defined. This study aimed to optimize the combinatorial parameters of aPDT, including the concentrations of MB (X1, 0.1-1.0 mM) and KI (X2, 100-400 mM), light dose (X3, 10-70 J/cm2), and MB's incubation time (X4, 5-35 min) for three Candida species. The best MB + KI-aPDT fungicidal effects (Y) against Candida albicans ATCC 90028 (YCa), Candida parapsilosis ATCC 22019 (YCp), and Candida glabrata ATCC 2950 (YCg) were investigated using a uniform design method. The regression models deduced using this method were YCa = 7.126 + 1.199X1X3 - 1.742X12 + 0.206X22 - 0.361X32; YCp = 10.724 - 0.867X1 - 1.497X2 + 0.560X3 + 1.298X22; and YCg = 0.892 - 0.956X1 + 2.296X3 + 1.299X42 - 3.316X3X4. The optimal combinatorial parameters inferred from the regression equations were MB 0.1 mM, KI 400 mM, a light dose of 20 J/cm2, and a 5-minute incubation time of MB for Candida albicans; MB 0.1 mM, KI 400 mM, a light dose of 70 J/cm2, and a 5-minute incubation time of MB for Candida parapsilosis; MB 0.1 mM, KI 100 mM, a light dose of 10 J/cm2, and a 35-minute incubation time of MB for Candida glabrata. The uniform design method can optimize the combinatorial parameters of aPDT mediated by MB plus KI to obtain the best aPDT fungicidal effects on Candida species, providing a new method to optimize the combinatorial parameters of aPDT for different pathogens in the future.