Carotenoids, including beta-carotene, are commercially valuable compounds, and their production by engineered Saccharomyces cerevisiae is a promising strategy for their industrial production. Here, to improve beta-carotene productivity in engineered S. cerevisiae, a cocktail delta-integration strategy, which involves simultaneous integration of various multi-copy genes, followed by selection of desirable transformants, was applied for modulation of beta-carotene production-related genes expression. The engineered strain, YPH499/Mo3Crt79, was constructed by three repeated rounds of cocktail delta-integration using CrtE, CrtYB, and CrtI derived from the yeast, Xanthophyllomyces dendrorhous. The recombinant strain produced 7.3 mg/L of carotenoids in 48 h and 52.3 mg/L of beta-carotene in 96 h, which were greater values than those achieved by CrtE, CrtYB, and CrtI co-overexpressing strains. Therefore, repeated cocktail delta-integration was effective in improving carotenoid productivity in S. cerevisiae and could be a promising technique for constructing metabolically engineered S. cerevisiae capable of producing bio-based chemicals.