Obesity is a major cause of nonalcoholic fatty liver disease (NAFLD), which is identified as a characteristic related to metabolic syndrome. This study focuses on the benefits of Scenadesmus dimorphus as a nutraceutical to overcome NAFLD-linked metabolic syndrome caused by obesity. The research used 30 mice (Mus musculus) divided into six groups: normal control, obesity control (OC), and drug control (Orlistat) and S. dimorphus administrated orally for 21 days in obese mice with NAFLD-linked metabolic syndrome with doses of 5 mg/20 g body weight (BW), 10 mg/20 g BW, and 15 mg/20 g BW. The administration of a high-fat diet can cause obese mice to suffer from NAFLD, resulting in an increase in liver enzymes and changes in lipid metabolism. Administration of S. dimorphus at 15 mg/20 g BW decreases the activity of liver enzymes and improves liver function. The statistics test showed significant differences (p < 0.05 analysis of variance) to decrease the liver enzyme activity of alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase compared to OCs. Administration of S. dimorphus resulting in metabolism changes showed a significant (at p < 0.05) decrease in total cholesterol, triglycerides, and low-density lipoprotein cholesterol and increased high-density lipoprotein cholesterol. Microalgae S. dimorphus is beneficial as a nutraceutical to manage obesity and reverse NAFLD-linked metabolic syndrome in obese mice.