The invention relates to a medical data duplicate checking and associating method and system. The method comprises the following steps of: (1) extracting core data items in to-be-processed medical data; (2) classifying the core data items; (3) respectively carrying out preliminary screening on the data items in an exclusion array and a fuzzy array; (4) carrying out deep screening on the data items in the core data items; (5) setting a threshold value M2 of a suspected duplicated data similarity and/or a threshold value M3 of suspected associated data; and (6) after artificially checking and judging the suspected duplicated and/or associated data, inputting the data which is judged as non-duplicated data into a medical database, and endowing the data which is judged to be associated with one or more corresponding association labels. Compared with the prior art, the method and system provided by the invention have the characteristics of being low in missed judging rate, low in wrong judging rate and high in duplicate checking efficiency, and do not have high requirement for the profession degree of artificial checking, so that the operation costs of the duplicate checking and associating are remarkably reduced.