Seborrheic dermatitis (SD) is a prevalent condition that results in dandruff, itching, and discomfort, and affect approximately 3–10% of the general population. Proliferation of the genus Malassezia, a microorganism inhabiting the scalp, is considered a contributing factor. Despite reducing the Malassezia population, other diseases, including SD, may still develop due to an increase in Staphylococcus aureus, which is associated with atopic dermatitis (AD) and SD, or a decrease in Staphylococcus epidermidis, which produces glycerol (moisturizer) and inhibits S. aureus growth. Therefore, we investigated the concentrations of anti-microbial reagents (pyrrolidone carboxylate-zinc [PCA-Zn] and Hinokitiol) and malt oligosaccharides (MT: corn-derived oligosaccharide mainly containing maltotetraose) that inhibited or promoted the growth of three types of scalp microorganisms. Individually, 0.50–1.00 mM PCA-Zn or 0.05–0.20 mM Hinokitiol displayed a marked growth-inhibitory effect on Malassezia furfur without a decline in S. epidermidis or an increase in S. aureus. Conversely, 0.02% MT individually exerted a growth effect on S. epidermidis but not on M. furfur. We then examined the effects of a mixture of the above-mentioned reagents on scalp-resident microorganisms. Our results indicated that 0.10 mM or 0.20 mM Hinokitiol combined with 0.02% MT markedly inhibited M. furfur growth and were the most effective at increasing S. epidermidis or decreasing S. aureus, compared to the single or combined effects of other reagents. Overall, our study provides valuable information on Hinokitiol and oligosaccharides concentrations in mixtures for use in shampoo-type cosmetics, and quasi-drugs, to prevent and treat SD.