To achieve high efficiency in microbial cell factories, it is crucial to redesign central carbon fluxes to ensure an adequate supply of precursors for producing high-value compounds. In this study, we employed a multi-omics approach to rearrange the central carbon flux of the pyruvate dehydrogenase (PDH) bypass, thereby enhancing the supply of intermediate precursors, specifically acetyl-CoA. This enhancement aimed to improve the biosynthesis of acetyl-CoA-derived compounds, such as terpenoids and fatty acid-derived molecules, in
Saccharomyces cerevisiae
. Through transcriptomic and lipidomic analyses, we identified
ALD4
as a key regulatory gene influencing lipid metabolism. Genetic validation demonstrated that overexpression of the mitochondrial acetaldehyde dehydrogenase (ALDH) gene
ALD4
resulted in a 20.1% increase in lipid production. This study provides theoretical support for optimising the performance of
S. cerevisiae
as a “cell factory” for the production of commercial compounds.