Micro-Tom is a miniature dwarf tomato, which can grow at a high density, has a short life cycle, and can be transformed efficiently. As a result, it became a new model plant for functional genomics study. The origin and biological characteristics of Micro-Tom were summarized. Recent advances in the mechanisms involved in the miniature dwarf trait, as well as the application of Micro-Tom in plant functional genomics study and the improved genetic transformation systems were reviewed.