The invention provides a method and system for assisting in disease diagnosis on the basis of intelligent inference, and relates to the field of computers. The method comprises the steps that input information of a user is obtained and analyzed, effective information in the input information is stored, the information matching degree of the effective information in a case library and the rule coverage rate of the effective information in a rule library are calculated, weighted summation is conducted on the information matching degree and the rule coverage rate, and an explaining value p of each disease in a disease library for the input information is obtained; diseases corresponding to the explaining values p are sorted according to the explaining values P, the disease of which the explaining value p is larger than or equal to a threshold value E serves as an initial inference conclusion to be returned to the user, inspection result information input by the user is obtained, diagnostic criteria, corresponding to the disease in the initial inference conclusion, in a book knowledge library are displayed to the user by combining the effective information. According to the method and system for assisting in the disease diagnosis on the basis of the intelligent inference, the process and form of an inquiry under the real scenario of clinical diagnosis are simulated, and the diagnosis result can be well explained.