Gardeniae fructus (GF), the fruit from Gardenia jasminoides Ellis, is a traditional Chinese medicine used for the treatment of nonalcoholic fatty liver disease (NAFLD) in the clinic. To explore the hepatoprotective mechanism of GF for the treatment of NAFLD, we proposed a novel strategy that integrated in vivo efficacy evaluation, network pharmacology analysis, molecular docking, and experimental validation. A NAFLD animal model induced by high fat diet (HFD) feed was established, then orally administrated with or without GF. The results showed that GF significantly decreased the levels of serum total cholesterol (TC), lipoprotein cholesterol, triglyceride (TG), alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, free fatty acids, glucose, and insulin and the levels of liver TG, TC, and malondialdehyde compared with the nontreated HFD group. Network pharmacology studies showed that quercetin, oleanolic acid, kaempferol, and geniposide were the main biocompounds in GF that targeted the PPARα and PPARγ genes through regulating the PPAR and AMPK signal pathways to protect against NAFLD. The interactions between bioactive compounds and their corresponding target proteins were analyzed by molecular docking and subsequently confirmed using the qRT-PCR assay. Collectively, GF was a therapeutic drug for the treatment of NAFLD.