The invention discloses an establishment method of a tobacco hairy root genetic transformation system. Comprising the steps of sterilizing tobacco seeds to obtain sterile tobacco seeds, germinating the tobacco seeds to obtain tobacco sterile seedlings, preparing agrobacterium, preparing agrobacterium infection liquid, infecting, co-culturing, sterilizing and culturing, screening and culturing to obtain tobacco hairy roots capable of being used for gene function detection, identifying the hairy roots and the like. The method is simple and easy to implement and short in period, enough hairy roots can be obtained in 8 weeks, and the obtained hairy roots can be applied to functional identification of tobacco genes (including detection of expression quantity of transformed genes; detection of the expression quantity of other target genes, detection of the content of nicotine, nornicotine, neonicotine and other tobacco substances); the technical problem that the traditional stable tobacco plant transformation from genetic transformation to T1-generation plants capable of being used for gene function identification takes a long time of about one year is solved; compared with the prior art, the tobacco hairy root genetic transformation system obviously shortens the research period.