Longan-flower-water-extract (LFWE) contains large amounts of phytochemicals where gentisic acid and epicatechin are the major compounds in phenolic acid and flavonoid compound, respectively. The objective of this study was to investigate if drinking LFWE could protect the liver from a hypercaloric dietary habit. Only rats fed the hypercaloric diet (HCD) with 25 g/L (w/v) LFWE solution (HCD_2X) group demonstrated lower (p < 0.05) serum triglyceride levels compared to those fed the HCD with normal distilled water (HCD_NDW) and HCD with 12.5 g/L (w/v) LFWE solution (HCD_1X) groups. However, drinking LFWEs decreased (p < 0.05) hepatic lipids in the HCD rats. Lower (p < 0.05) hepatic MDA levels, GOT and GPT values, and higher (p < 0.05) hepatic GSH levels were observed in HCD rats drinking LFWE. Besides, drinking LFWE downregulated (p < 0.05) gene expressions and activities of hepatic matrix metalloproteinases-2 and -9 (MMP-2/9) in HCD rats. In conclusion, polyphenol-rich LFWE displayed hepatoprotective characteristics against an energy-dense dietary habit.