Recently, deep learning has produced encouraging results for kidney stone classification using endoscope images. However, the shortage of annotated training data poses a severe problem in improving the performance and generalization ability of the trained model. It is thus crucial to fully exploit the limited data at hand. In this paper, we propose SegPrompt to alleviate the data shortage problems by exploiting segmentation maps from two aspects. First, SegPrompt integrates segmentation maps to facilitate classification training so that the classification model is aware of the regions of interest. The proposed method allows the image and segmentation tokens to interact with each other to fully utilize the segmentation map information. Second, we use the segmentation maps as prompts to tune the pretrained deep model, resulting in much fewer trainable parameters than vanilla finetuning. We perform extensive experiments on the collected kidney stone dataset. The results show that SegPrompt can achieve an advantageous balance between the model fitting ability and the generalization ability, eventually leading to an effective model with limited training data.