Plant leaf identification is crucial for biodiversity protection and conservation and has gradually attracted the attention of academia in recent years. Due to the high similarity among different varieties, leaf cultivar recognition is also considered to be an ultra-fine-grained visual classification (UFGVC) task, which is facing a huge challenge. In practice, an instance may be related to multiple varieties to varying degrees, especially in the UFGVC datasets. However, deep learning methods trained on one-hot labels fail to reflect patterns shared across categories and thus perform poorly on this task. To address this issue, we generate soft targets integrated with inter-class similarity information. Specifically, we continuously update the prototypical features for each category and then capture the similarity scores between instances and prototypes accordingly. Original one-hot labels and the similarity scores are incorporated to yield enhanced labels. Prototype-enhanced soft labels not only contain original one-hot label information, but also introduce rich inter-category semantic association information, thus providing more effective supervision for deep model training. Extensive experimental results on public datasets show that our method can significantly improve the performance on the UFGVC task of leaf cultivar identification.