The invention discloses a method and a system for automatically establishing a medical term mapping relationship based on word segmentation and coding. The method comprises establishing the mapping relationship between terms of a dictionary A and terms of a dictionary B, and specifically comprising the steps of 1, dividing each sample term into a main field and an attribute field; 2, establishing a main field table by the main fields and codes obtained in the step 1, and establishing a word segmentation dictionary by common Chinese characters and the attribute fields; 3, performing Chinese word segmentation on words in the main field table; 4, performing Chinese word segmentation on the terms of the dictionary A; 5, computing correlation degree between the main field of each sample term and the main field of the corresponding term of the dictionary A; 6, matching and coding the main fields of the sample terms and the main fields of the terms of the dictionary A according to the correlation degrees; and 7, coding the main fields of the terms of the dictionary B, and establishing the mapping relationships aiming at the terms, with the same main field codes, of the dictionary A and the dictionary B. According to the method, the problem that the manual term mapping efficiency is low thus medical information is difficult to be shared is solved.