The detection of bolts is an important task in high-speed train inspection systems, and it is frequently performed to ensure the safety of trains. The difficulty of the vision-based bolt inspection system lies in small sample defect detection, which makes the end-to-end network ineffective. In this paper, the problem is resolved in two stages, which includes the detection network and cascaded classification networks. For small bolt detection, all bolts including defective bolts and normal bolts are put together for conducting annotation training, a new loss function and a new boundingbox selection based on the smallest axis-aligned convex set are proposed. These allow YOLOv3 network to obtain the accurate position and bounding box of the various bolts. The average precision has been greatly improved on PASCAL VOC, MS COCO and actual data set. After that, the Siamese network is employed for estimating the status of the bolts. Using the convolutional Siamese network, we are able to get strong results on few-shot classification. Extensive experiments and comparisons on actual data set show that the system outperforms state-of-the-art algorithms in bolt inspection.