The invention relates to a method for identifying cigarettes by using electrochemical fingerprints. The method comprises the steps that cut tobacco of cigarettes of different varieties and cigarettes to be identified are taken respectively, dried and cooled, and then are stirred by adding an extracting solution inside and filtered, and the filtrate is collected, or the filtered cut tobacco is cooled and then ground into powders to obtain a standard sample and a sample to be identified; then an appropriate amount of the standard sample or the sample to be identified is taken and added into a B-Z oscillating system with a constant temperature, and the electrochemical fingerprints are obtained with a platinum electrode as the indicating electrode and a double salt bridge saturated calomel electrode or Ag/AgCl electrode as the reference electrode; and the characteristic parameters of the standard sample and the sample to be identified are extracted according to the electrochemical fingerprints, and the category or the genuine or whether the counterfeit of the sample to be identified is a counterfeit is identified by using such as pattern recognition methods as an artificial neural network. With the method of the invention, the treatment of samples is simple, the cost is low, the identification speed is fast, the operation is simple and convenient, and the results are accurate and reliable; and the method can be used for identifying the varieties and whether the cigarette is a counterfeit.