Abstract:[Background] Hongjundouzha was a traditional delicacy unique to the Hakka region of western Fujian. [Objective] To analyze the compound transformation and special flavor formation during the fermentation process of the Hakka traditional fermented food Hongjundouzha. [Methods] Analyzedthe sensory characteristics of Hongjundouzha samples collected at different time points of fermentation. GC-MS/MS-based widely targeted metabolomics, RNA-seq-based transcriptomics, and Label-Free quantitative proteomics were used to analyze the flavor composition of samples and identify the main differentially expressed genes and proteins that affect strain fermentation. [Results] A total of 198 flavor compounds were obtained from the samples at different time points of fermentation, mainly including (E,E)-2,4-decadienal, (E)-2-hexenal, 1-octanol, azulene, and 2-pentylfuran. Day two of fermentation was the main period for transcription and expression of genes involved in the fermentation with Neurospora crassa, with the most genes involved in the fermentation process of Hongjundouzha samples. The number of differentially expressed genes and proteins screened out was the highest (2 814 and 415, respectively) on this day. On day three of fermentation, the sample tended to become mature, and the number of genes and proteins involved in the fermentation process was the least, at 99 and 43, respectively. From day two to three, the strain underwent metabolism of starch and sugars, synthesis of amino acids, and metabolism of fatty acids, which were accompanied by a decrease in the beany smell and the production of alcohols, ketones, and esters with special aromas, resulting in a sustainable sense of freshness (richness) and sweetness in the sample. At the same time, the hardness, shear strength, and chewiness of the sample increased. On day four, the Hongjundouzha sample began to produce some oils indicating food spoilage and compounds such as chlorocyclohexane and nitrocyclohexane, causing the sample to age and the product quality to decline. [Conclusion] This study utilized multiomics to elucidate the composition and transformation of flavor compounds in Hakka Hongjundouzha at different time points of fermentation from a molecular level. This can lay a foundation for improving the fermentation efficiency and quality of Hongjundouzha, promoting the deep processing of value-added products, and moving towards industrial production.