The invention relates to a multi-form medical image data labeling method and system, and the method comprises the steps: receiving a picture uploaded by a user, and checking whether the format is correct or not according to a preset picture format; if yes, uploading the picture, and if not, reminding the user to upload the picture again; extracting picture information to be matched with an information base, and judging whether the picture has annotation or attribute information or not; setting the permission of labeling the picture; providing a labeling tool box for the user according to the disease type; receiving annotation information of the user on the picture, and uploading and storing the annotation information; extracting annotation information of users of the same level for the picture, comparing the annotation information, judging whether the annotation information of the users of the same level is different or not, if not, generating a final annotation result, and if yes, submitting the final annotation result to a next-level user for further annotation. According to the method and system, different labeling tools can be used for labeling images, the labeling requirementsof medical images in various forms are met, and the accuracy of image labeling is improved by adopting a hierarchical labeling process.