To enable automatic transplantation of plug seedlings and improve identification accuracy, an algorithm to identify ideal seedling leaf sets based on Fourier descriptors is developed, and a classification method based on expert system is adopted to improve the identification rate of the plug seedlings. First, the image of the plug seedlings is captured by image acquisition system, followed by application of K-means clustering for image segmentation and binary processing and identification of the ideal seedling leaf set by Fourier descriptors. Then we obtain feature vectors, such as gray scale (R+B+G)/3, hue H, and rectangularity. After that the knowledge model of the plug seedlings is defined, and the inference engine based on knowledge is designed. Finally, the recognizing test is carried out. The success rate of the identification of 10 varieties of plug seedlings from 190 plates is 98.5%. For the same sample, the recognizing rate of support vector machine (SVM) is 85%, the recognizing rate of particle-swarm optimization SVM (PSOSVM) is 87%, the recognizing rate of back propagation neural network (BP) is 63%, and the recognizing rate of Fourier descriptors SVM (FDSVM) is 87%. These results show that our recognition method based on an expert system satisfies the requirements of automatic transplanting