Black tea is a kind of full-fermented tea with therapeutic potential for metabolic diseases. Ectopic lipid deposition (ELD) is an essential risk factor for organ injury in metabolic syndrome, especially in liver and kidney, for which effective interventions are lacking. Here, we explored whether black tea extract (BTE) improves fatty liver and fatty kidney, as well as identified the potential lipid biomarkers for ELD and lipid targets of BTE on the improvement of ELD. Transcriptome data from diet-induced obese mice were analyzed to confirm high-fat-diet feeding disturbs lipid metabolism in the liver and kidney. BTE prominently inhibited body weight gain, improved glucose metabolism, as well as reduced lipid droplet accumulation in the liver and kidney. Moreover, lipidomic profiling analyses identified 28 lipid classes in the liver while 29 in the kidney with that up-regulated glycerides and phosphatidylcholines, as well as down-regulated cardiolipin were the characteristic changes in ELD. BTE prominently reduced glycerides in ELD, thereby constituting the basis of its anti-ELD effect. Specifically, BTE displayed stronger effects on lowering cholesterol ester (CE) in fatty liver, while also affecting phospholipids and sphingolipids in fatty kidney. Ultimately, integrative analysis identified CE18:2 and triglyceride (TAG)56:4 (20:2) as the potential lipid biomarkers for BTE in improvement of ELD. BTE could be an effective food supplement for the prevention and treatment of ELD. Notably, CE18:2 and TAG56:4(20:2), as the potential lipid biomarkers, may facilitate the research and development of anti-ELD drug.