The invention discloses a system and a method for searching a biomedical flow chart basing on content and structure. The system comprises a structure extracting module, an OCR (Optical Character Recognition) module, a storage module, a LUCENE searching module, a similarity measurement module, a hand-drawing flow chart input module, a display module and the like. The method is carried out in a way that (1) characters in the biomedical flow chart can be extracted by adopting a character recognition technology, a traditional mode of manually annotating an image is avoided, the implementation is convenient and fast, and the error rate is low; (2) the structure information of the biomedical flow chart is fully utilized, the specific structure information of the biomedical flow chart can be used as a searching condition, and the accuracy of searching the biomedical flow chart can be increased.