A yeast starter is formulated for commercial practices, including storage and distribution. The cell viability of the yeast starter is one of the most important factors for manufacturing alcoholic beverages to ensure their properties during the fermentation and formulation processes. In this study, 64 potential protective agents were evaluated to enhance the survival rate of the brewing yeast Saccharomyces cerevisiae 88-4 after freeze-drying. In addition, the optimized combination of protective agents was assessed for long-term storage. Finally, response surface methodology was applied to investigate the optimal concentration of each protectant. Twenty of the 64 additives led to an increase in the survival rate of freeze-dried S. cerevisiae 88-4. Among the various combinations of protectants, four had a survival rate >95%. The combination of skim milk, maltose, and maltitol exhibited the best survival rate of 61% after 42 weeks in refrigerated storage, and the composition of protectants optimized by response surface methodology was 6.5–10% skim milk, 1.8–4.5% maltose, and 16.5–18.2% maltitol. These results demonstrated that the combination of multiple protectants could alleviate damage to yeasts during freeze-drying and could be applied to the manufacturing starters for fermented foods.