Honey is a precious natural product with high nutritional and medicinal values, which both depend on its botanical origin. However, honey is susceptible to adulteration and false labeling claims of plant origin, its botanical origin certification has become a global challenge due to the complex nature of honey and the various types of adulteration. Therefore, it is crucial to establish accurate, rapid, and comprehensive methods for identifying the botanical origin of honey to ensure its quality. Foodomics, one of the most rapidly developing technologies in recent years, is a powerful tool for determining food components and nutrients at the molecular level. It is increasingly used in honey authentication due to its advantages, such as high throughput and wide applicability. This review provides an overview of the research progress made in authenticating the botanical origin of honey using omics techniques over the past decade (2013–2023). This paper describes the differences in the chemical composition and sensory characteristics of honey from different plant varieties. It is found that metabolomics has been widely used in honey plant origin identification studies, and current studies mainly apply various advanced instruments combined with different chemometrics to discover unique markers or establish classification models. It is strongly recommended to apply multiple omics analysis techniques jointly to increase the compound coverage, to explore the metabolic pathways and changes of metabolites from plants to honey, and then to its maturity throughout the process, to provide comprehensive information for future omics studies.