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Zhenba bacon is a traditional dry-cured product with rich nutritive values. The fat oxidation is the main way to produce flavor substances and is often closely related to fat distribution in bacon production. The purpose of this study was to reveal the reason of the influence of fat distribution (pork belly and rump meat) on the flavor substances of Zhenba bacon. Processing samples from pork belly (LRW) and pork rump (LRT) at different smoking periods (8, 24 and 40-day) were analyzed by untargeted metabolomics and gas chromatography-ion mobility spectrometry (GC-IMS), and correlations between differential metabolites and key volatile flavor compounds were assessed. The GC–IMS results revealed that the content of 1-butanol, 1-pentanol, benzaldehyde, and furfural was the highest in LRW sample, the content of 3-methyl-3-buten-1-ol, 1-penten-3-ol, linear aldehyde and acetic acid ethyl ester was the highest in LRT sample. Metabolites analysis identified that the metabolites with significant differences were mainly lipid substances, organic acids and derivatives. KEGG pathway enrichment showed that the differential metabolites were related to the metabolism of various types of amino acids. The results could provide data support and theoretical reference for improving the processing technology of Zhenba bacon.