Higher alcohols (phenylethyl alcohol and isoamyl alcohol), as the crucial aroma compounds, have been found to associate with the sensory properties of various alcoholic products. The Ehrlich and Harris pathways are the main pathways for yeast to produce phenylethyl alcohol and isoamyl alcohol during the brewing process of alcoholic products, whereas the specific changes of the Ehrlich and Harris pathways in Wickerhamomyces anomalus under ethanol stress are still unclear. In this study, W. anomalus NCU003 with a high capacity for aroma compound production was treated with ethanol stress at different concentrations (3%, v/v, 6%, v/v and 9%, v/v) to study the effects on the expression levels of genes and metabolite content in the Ehrlich and Harris pathways. The results found that ethanol stress inhibited the production of phenylethyl alcohol and isoamyl alcohol, and the content decreased with the increase of ethanol concentrations. In the meantime, the up‐regulation of ARO1, CS, ARO8, Leu1, BAT2 and ilvs family genes in the Ehrlich and Harris pathways could lead to an increase in the synthesis of important precursor substances during the synthesis of phenylethyl alcohol and isoamyl alcohol. However, the significant down‐regulation of ARO10, PDC, ADH1 and AHD2 genes was the main reason for the low production of phenylethyl alcohol and isoamyl alcohol. These results could provide a theoretical reference for the construction of genetic engineering strains of W. anomalus in the future so as to reasonably control the content of higher alcohols during the brewing process of alcoholic products.