Polycyclic aromatic hydrocarbon exposure contributes most to the initiation and progression of lung cancer. Metabolic reprogramming is an important hallmark of tumors and essential for the malignant transformation and progression of lung cancer. However, benzo[a]pyrene-induced metabolic reprogramming of lung cancer cells during the invasion and migration is still unclear. Accordingly, benzo[a]pyrene (5 μg/L, within the range of the equivalent dose of polycyclic aromatic hydrocarbons in human blood), was used to induce the invasion and migration of large cell lung cancer H460 cells. Subsequently, an untargeted metabolomics approach using ultra-high-performance liquid chromatograph-mass spectrometry was conducted to discover benzo[a]pyrene-induced metabolic reprogramming of H460 cells and potential therapeutic targets. We showed that 117 of 202 identified metabolites were significantly altered in H460 cells upon benzo[a]pyrene exposure. Subsequent pathway analysis revealed that 31 metabolic pathways were significantly altered in benzo[a]pyrene-exposed H460 cells. Notably, 11 fatty acids (10–22 carbons) and 6 purine nucleotides accumulated, while acylcarnitines (6–18 carbons), most phospholipids (such as lysophosphatidylcholines, lysophosphatidylethanolamines, lysophosphatidylinositols and phosphatidylcholines) and sphingolipids (such as sphingomyelins and sphingosines) were decreased in benzo[a]pyrene-exposed H460 cells. Besides, 14 amino acid metabolic pathways were significantly altered in benzo[a]pyrene-exposed H460 cells, such as glutathione metabolism, alanine, aspartate and glutamate metabolism, tryptophan metabolism, and arginine and proline metabolism. Spearman correlation analysis and correlation networks demonstrated high correlations of fatty acids, acylcarnitines, phospholipids, sphingolipids, nucleotides and amino acids with H460 cell invasion and migration. This study suggests fatty acid metabolism, phospholipid metabolism, sphingolipid metabolism, amino acid metabolism and nucleotide metabolism as potential therapeutic targets for intervening the toxic effects of polycyclic aromatic hydrocarbons and related diseases. To our knowledge, decreases in acylcarnitines (6–18 carbons), phospholipids and sphingolipids, and accumulation of fatty acids and purine nucleotides are novel phenomena in benzo[a]pyrene-exposed large cell lung cancer cells.