Background: Jiangzhi Decoction (JZD), a traditional herb mixture, has shown significant clinical efficacy against non-alcoholic fatty liver disease (NAFLD). However, its multicomponent and multitarget characteristics bring difficulty in deciphering its pharmacological mechanisms. Our study aimed to identify the key active ingredients and core molecular mechanisms of JZD against NAFLD. Methods: The active ingredients were searched from Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and Traditional Chinese Medicine Integrated Database (TCMID). The targets of those ingredients were identified using ChemMapper database based on 3D-structure similarity. NAFLD-related genes were searched from DisGeNET database and Gene Expression Omnibus (GEO) database. Then we obtained candidate targets of JZD against NAFLD by overlapping the active ingredient targets and NAFLD-related genes. We performed protein-protein interaction (PPI) analysis, functional enrichment analysis and constructed pathway networks of “herbs-active ingredients-candidate targets”, and identified the key active ingredients and core molecular mechanisms in the network. Results: We found 147 active ingredients in JZD, 1285 targets of active ingredients, 401 NAFLD-related genes, and 59 overlapped candidate targets of JZD against NAFLD. 22 core targets were obtained by PPI analysis. Finally, nuclear receptor transcription and lipid metabolism regulation were found as the core molecular mechanisms of JZD against NAFLD by functional enrichment analysis, and emodin, emodin anthrone, hyperin, questin, rhein, etc. were speculated as the key active ingredients of JZD. Conclusion: Our study will provide the scientific evidences of the clinical efficacy of JZD against NAFLD.