Metabolic dysfunction associated fatty liver disease (MAFLD), a globally prevalent chronic liver disease, has only limited pharmacological options. Both metformin and Ganwei, a botanical supplement containing a potent inducer for glycine N-methyltransferase (GNMT), have shown great promise for MAFLD. We conducted a 4-arm, randomized, placebo-controlled trial to investigate the safety and efficacy of metformin and Ganwei for MAFLD. Between September 2021 and March 2023, 64 patients with MAFLD were received metformin alone, Ganwei alone, combination of metformin and Ganwei, and placebo for 6 months. The primary MAFLD outcome was assessed by control attenuation parameter (CAP) and kilopascal (kPa) scores for liver steatosis and fibrosis, utilizing FibroScan. At 6 months after treatment, significant MAFLD improvements were observed in patients treated with Ganwei alone (repeated measures ANOVA test, p = 0.048 for both CAP and kPa scores). By employing a 6-point steatosis grade scale, the Ganwei alone arm exhibited a statistically better improvement than the placebo-controlled arm (mean score 1.1±1.9 vs. 0.1±0.7, p < 0.01). In addition, patients in the Ganwei alone arm showed significant quality-of-life improvements. There was no serious adverse events observed. Our study demonstrated that Ganwei can be an effective treatment option for MAFLD patients. Clinical trial registration: NCT06244550.