6-Benzylaminopurine (6-BA) is ubiquitous in agricultural production and is accessible to humans through diets. The modulation of lipid metabolism by 6-BA has been previously demonstrated in plants and oleaginous microorganisms. Therefore, whether it alters lipid homeostasis in other living organisms requires further investigation. In this study, doses ≥10 mg 6-BA/L caused malformation of the yolk sac, steatosis, and other hepatopathies in zebrafish larvae. Exposure to 25 mg 6-BA/L resulted in increased levels of triglyceride and total cholesterol. Results of transcriptomic analysis indicated that 6-BA alters genes associated with fatty acid and glycerophospholipid metabolism. Among them, the expression levels of hmgcra, elovl7b, and apobb.2 were downregulated, whereas those of lpcat3, bco1l, cyp7al, fabp1b.1, elp6, pde6ha, apoa4b.2_2, sgk1, dgkaa, and mogat2 were upregulated. Correspondingly, a study of the metabolome identified lysophosphatidylcholine (LPC) as the major differentially expressed metabolite in response to 6-BA treatment. Therefore, abnormal accumulation of LPCs and dyshomeostasis of glycerophospholipid metabolism were identified as potential mechanisms causing the toxicity of 6-BA, which should be assessed to understand the risks of 6-BA and the products contaminated by it. Environmental implication: 6-Benzylaminopurine (6-BA), an important residue in “toxic bean sprouts,” is ubiquitous in agricultural production and is common in typical diets. Its regulation of lipid metabolism has been demonstrated in plants and oleaginous microorganisms. Whether it alters lipid homeostasis in other organisms and the underlying mechanisms remain largely unknown. The worldwide use of 6-BA and the potential exposure of humans have aroused public attention owing to its hazardous effects; thus, its hazardous effects, particularly those on lipid homeostasis, deserve careful clarification.