260 unenhanced abdominal CT scans from 2018 to 2020 were collected from the First Affiliated Hospital of Guangzhou Medical University. After data desensitization and data cleaning, the clean NIfTI image of abdominal CT scans was annotated based on clinical requirements and image segmentation needs. Two labels (“kidney” and “kidney stone”) were considered for masking and labeling. The 3D Slicer tool was used to mask the CT scans. The data annotations process comprised three stages. Data annotation was performed under the guidance of a professional urologist. Each CT scan contains an original raw image and a masked image for kidney and kidney stone. Please note that the whole dataset is split into 5 parts for easy download.