The efficient and stable genetic transformation system of plants is an important technical support for gene function analysis and molecular breeding. The lack of a complete tissue culture system has seriously hindered its application in many plants, especially crops. In recent years, many efficient non-tissue culture genetic transformation systems have been established to solve the above problems. This review focuses on the application of Agrobacterium-mediated non-tissue culture genetic transformation systems, including flower organ infection, cut-dip-bud (CDB) delivery, regenerative activity–dependent in planta injection delivery (RAPID), seed infection, developmental regulatory (DR) gene assisted transformation and virus delivery in plants, the influencing factors of transformation efficiency and gene editing applications. The application of pollen tube channel method, particle bombardment method and nano delivery method in plants independent of Agrobacterium is summarized. This review will provide reference for more species to establish efficient, simple and genotype-independent non-tissue culture genetic transformation system, and help plant functional gene research and molecular breeding practice.