Abstract: To elucidate the metabolic mechanism by which Enterobacter hormaechei can improve the quality of fermented tobacco leaves, non-targeted metabolomics technology was employed to systematically analyze the metabolic transformations and key functional pathways driven by Enterobacter hormaechei during the solid-state fermentation procedure of tobacco leaves. Using tobacco leaves (C3F-AB 2022) from the Baoji tobacco planting area of Shaanxi Province as the material, and the high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-QTOF-MS) technology was applied. Differential metabolites during the 0–72 h fermentation of tobacco leaves by Enterobacter hormaechei were screened using partial least squares discriminant analysis (PLS-DA), and the key metabolic pathways were elucidated using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results showed that: 1) A total of 945 metabolites were identified, with 151 significantly differential metabolites screened, including glucose, amino acids, organic acids, and terpenoids, etc. 2) The differential metabolites were enriched in 129 pathways, such as biosynthesis pathway of phenylalanine, tyrosine, and tryptophan, biosynthesis pathway of terpenoid and quinone, etc. Among these, five pathways (such as biosynthesis of terpenoids and quinones, metabolism of phenylalanine, metabolism of galactose) were significantly related with the quality improvement. Non-targeted metabolomics analysis revealed that the growth and metabolism of Enterobacter hormaechei drive the transformation of differential metabolites by enriching key pathways, such as terpenoids synthesis and phenylalanine metabolism, thereby improving the quality of tobacco leaves.