The invention provides an intelligent specimen collection method and system. The method comprises the following steps: acquiring first identification information of a to-be-collected user, the first identification information being associated with to-be-collected specimen information of the user, and the to-be-collected specimen information including the specimen collection quantity and the type of a specimen container; detecting whether second identification information of the specimen container is matched the to-be-collected specimen information, and when the identification information in the specimen container is matched with the to-be-collected specimen information, utilizing the specimen container to perform collection, and associating the second identification information with the user; otherwise, generating an alarm signal to warn misoperation. Manual active judgment is not needed in the whole process, and a collected object and the specimen container are scanned and identifiedby a terminal, double detection is adopted to avoid manual checking of misoperation, and the identification efficiency and the degree of accuracy are improved.