Display omitted •Real samples were collected throughout the entire solid-state fermentation process.•Establish a consistent pesticide residue monitoring system.•Verified for the distribution of pesticides in samples based on key node samples.•Elucidate the rules of pesticide residues during the product process of baijiu.•Find the input and eliminate pathways for pesticides during solid-state fermentation. By collecting real samples throughout the entire production process and employing chemometrics, metabolomics, and modern separation omic techniques, it unveiled the patterns of pesticide transfer during solid-state fermentation. The results indicated that 12 types of pesticide residues were prevalent during baijiu production, with organochlorine and carbamate pesticides being the most abundant in raw materials. After fermentation, organochlorine pesticides and pyrethroid pesticides exhibited higher content, while carbamate pesticides dominated in the final product. The pathways for pesticide input and elimination were identified, and the intricate mechanisms underlying these changes were further elucidated. Additionally, key control points were defined to facilitate targeted monitoring. The results indicated that pesticide residue primarily originates from raw materials and Daqu, whereas both solid-state fermentation and distillation processes were effective in reducing pesticide residues. The study offers valuable guidance for establishing pesticide residue standards in the context of baijiu production.