Lingguizhugan Decoction (LGZG) has been investigated in basic studies, with satisfactory effects on
insulin resistance in
non-alcoholic fatty liver disease (
NAFLD). This translational approach aimed to explore the effect and underlying mechanism of LGZG in clinical setting. A randomized, double-blinded, placebo-controlled trial was performed. A total of 243 eligible participants with
NAFLD were equally allocated to receive LGZG (two groups: standard dose and low dose) or placebo for 12 weeks on the basis of lifestyle modifications. The primary efficacy variable was homeostasis model assessment of
insulin resistance (HOMA-IR). Analyses were performed in two populations in accordance with body mass index (BMI;
overweight/obese, BMI ⩾ 24 kg/m2; lean, BMI < 24 kg/m2). For
overweight/obese participants, low-dose LGZG significantly decreased their HOMA-IR level compared with placebo (-0.19 (1.47) versus 0.08 (1.99), P = 0.038). For lean subjects, neither dose of LGZG showed a superior effect compared with placebo. Methylated
DNA immunoprecipitation sequencing and real-time qPCR found that the
DNA N6-methyladenine modification levels of
protein phosphatase 1 regulatory subunit 3A (PPP1R3A) and autophagy related 3 (ATG3) significantly increased after LGZG intervention in
overweight/obese population. Low-dose LGZG effectively improved
insulin resistance in
overweight/obese subjects with
NAFLD. The underlying mechanism may be related to the regulation of
DNA N6-methyladenine modification of PPP1R3A and ATG3. Lean subjects may not be a targeted population for LGZG.