This paper presents a new approach called the empirical mode decomposition-window fractal (EMDWF) algorithm in classification of fingerprint of medicinal herbs. In this way, we consider a glycyrrhiza fingerprint of medicinal herb as a signal sequence, and apply empirical mode decomposition (EMD) and Hiaguchis fractal dimension to construct a feature vector. By using EMD, the glycyrrhiza fingerprint of medicinal herb can be decomposed into some intrinsic mode functions (IMFs). As window fractal dimension (WFD) is applied to each IMF and original signal, the features of the glycyrrhiza fingerprint of medicinal herb can be obtained. Thereafter, SVM is applied as a classifier. The results of the experiments state clearly that the feature extracted by EMDWF is better than that of the existing methods including the pure EMD. With the increase of the number of training samples and the increase of the number of layers in EMD, the classification result achieves more stability.