The increase in industrialization has led to a significant energy crisis, sparking interest in lignocellulosic biomass for fuel ethanol production because of its renewable characteristics. The complex composition of this biomass requires pretreatment to reduce inhibitors like furfural and hydroxymethylfurfural (HMF), which hinder enzymatic hydrolysis and fermentation, ultimately decreasing ethanol yields. This study investigates the detoxification mechanisms of furan aldehydes in Scheffersomyces stipitis, particularly through the upregulation of genes SsOYE2.2, SsOYE2.7, and SsOYE3.1 under furfural and HMF stress. Enzyme characterization determined that SsOye3.3p is the most active enzyme for reducing both compounds using NADPH. Notably, SsOye2.6p showed the highest catalytic efficiency towards furfural, while SsOye2.8p was optimal for HMF. The study also established the optimal temperature and pH for these enzymatic reactions. Importantly, SsOye2.5p displayed broad substrate specificity, indicating its potential in detoxifying various aldehydes in microbial cells. The findings suggest that genes linked to enhanced enzymatic properties were not significantly induced, indicating that S. stipitis has more substantial potential for furan aldehyde detoxification and can be developed as a chassis organism exhibiting furan aldehyde tolerance. These insights facilitate the development of novel enzymes to counter furan aldehyde inhibitors and the creation of furan aldehyde-tolerant strains via genetic engineering.