Saccharomyces cerevisiae is a widely used cell factory for the production of fuels and chemicals. However, as a non-oleaginous yeast, S. cerevisiae has a limited production capacity for lipophilic compounds, such as beta-carotene. To increase its accumulation of beta-carotene, we engineered different lipid metabolic pathways in a beta-carotene producing strain and investigated the relationship between lipid components and the accumulation of beta-carotene. We found that overexpression of sterol ester synthesis genes ARE1 and ARE2 increased beta-carotene yield by 1.5-fold. Deletion of phosphatidate phosphatase (PAP) genes (PAH1, DPP1, and LPP1) also increased beta-carotene yield by twofold. Combining these two strategies resulted in a 2.4-fold improvement in beta-carotene production compared with the starting strain. These results demonstrated that regulating lipid metabolism pathways is important for beta-carotene accumulation in S. cerevisiae, and may also shed insights to the accumulation of other lipophilic compounds in yeast.