The prevalence rate of nonalcoholic fatty liver disease (NAFLD) reaches up to 30% around the world, and the disease has a serious impact on human health and constitutes a public health burden. Due to difficulties in the diagnosis and monitoring of NAFLD, it is important to identify potential drug targets and biomarkers, and multi-omics techniques hold great promise in the search for early diagnostic markers, therapeutic targets, and outcome and prognostic assessment of NAFLD. This article reviews the research advances in multi-omics techniques in the field of NAFLD in recent years, in order to provide a richer theoretical basis and new strategies for the prevention and treatment of NAFLD.