The invention provides a fingerprint identification method of an industrial control scanner based on honeynet data, comprising the following steps: scanning data captured through a honeypot network system in an industrial control network and an existing industrial control scanner are analyzed to obtain fingerprint information and a multi-classifier model of scanning data based on a CART decision tree is constructed. The multi-classification classifier model can effectively identify the specific scanning tools that initiate the scanning traffic and output the judgment probability of various scanner tags. After that, the output of the multi-classification classifier model will be used as the input data of the clustering algorithm. The clustering algorithm can discover the deeper relationshipbetween different scanning entities and form clustering. At the same time, the clustering algorithm can effectively extract scanning features of different clusters, form new scanner tags, and updatethem to the previous multi-classification decision tree, thereby improving the judgment ability of the invention for the novel scanner data.