The present invention discloses a medical big data based disease automatic assistance diagnosis system and method. The system comprises: a background data storage unit; an information processing unit, which specifically comprises: a statistical classification module, used for acquiring case data in the background data storage unit, and performing statistical classification on the case data, so as to obtain a symptom set and a definitively diagnosed disease type set; a diagnosed disease set calculation module, used for calculating a definitively diagnosed symptom set of various diseases according to the symptom set and the disease type set that are obtained by the statistical classification module; and a disease automatic diagnosis module, used for acquiring disease symptom data provided by a user, generating a selection symptom set, comparing the selection symptom set with the definitively diagnosed symptom set of various diseases and performing calculation, so as to obtain a disease determination result; and a man-machine interaction unit, used for displaying an interface of selecting a disease by the user, and outputting a disease diagnosis result. The method disclosed by the present invention is simple, easy and strong in operatability, and provides a new clinic assistant diagnosis tool for the medical field, and reduces an error/miss diagnosis rate.