The invention discloses a system for evaluating the similarity of digital chromatographic fingerprint of Chinese medicine, which includes the test of the substances by HPLC, input of the test result into the digital computer which saves programs, the digital computer which saves programs executes the following step: inputting data of quality goods and tested samples being tested by the HPLC into the original database, matching the data of quality goods and tested samples with the standard data, forming a quality goods fingerprint collection, a quality goods characteristic fingerprint database and a tested sample fingerprint collection; processing peak matches between the data in the tested sample fingerprint collection with the data in the quality goods characteristic fingerprint database, forming a tested sample fingerprint database, calculating the similarity between the quality goods and the similarity between the tested samples and every quality good, if the similarity mean of the tested samples is larger than the similarity mean J of the quality goods characteristic fingerprint database, the product is a qualified product, compared with the prior art, the peak-to-peak comparability is improved, the scientific processing is combined with integrity and fuzzyness, the datamation of the map is realized.