Obesity and dyslipidemia incidences have increased in the general population in line with the increase in fat consumption. These conditions contribute to systemic organ disruption, including the kidney, as a result of lipid imbalance and systemic inflammation that occur. Clitoria ternatea (CT) flower is found to have rich flavonoid content and potentially reduce obesity and dyslipidemia-related complications through inhibition of HMG-CoA reductase, the precursor enzyme for cholesterol synthesis. This study aims to determine the potency of CT aqueous extract in ameliorating kidney damage in rats with high-fat diet. An experimental study was conducted involving 25 Wistar rats which were divided into a normal group (ND), a high-fat diet (HFD) group, and three of the treatment groups with CT extract (HFD+CT250; HFD+CT500; HFD+CT750). We harvested the kidney then processed histological preparation and valued it by using ImageJ software. Phytochemical and molecular docking analysis was also performed. CT extract was found to have 1771,39 mg/100g flavonoid content. Macroscopic examination showed a significant reduction of kidney weight in the HFD+CT750 groups compared to the HFD group (1.65±0.30 vs 2.26±0.47 g; p= 0.02). The amelioration of kidney morphology was represented by a significant reduction in Bowman’s space of the HFD+CT500 group compared to the HDF group (0.53±0.39 vs 3.78±1.03 μm; p= 0.018). CT extract is also able to inhibit the glomerular tuft area enlargement with the similar area compared to the ND group (31.28±8.51 vs 20.0±4.26 μm; p= 0.3). Docking analysis shows that delphinidin, a type of flavonoid on CT extract, has the potency to inhibit HMG-CoA reductase with lower bonding energy compared to simvastatin (-8.0 vs -7.0 kcal/mol) thus showing the potency to inhibit dyslipidemia-related condition. Clitoria ternatea extract has rich flavonoid content with potentially ameliorates kidney morphology damage through inhibition of HMG-CoA reductase in rats with high-fat diet.