The invention provides a similarity analysis method and system for patients suffering from cardio-cerebral vascular diseases. The method comprises the following steps of 1 problem definition, wherein problem definition for the patients suffering from the cardio-cerebral vascular diseases is conduced; 2 data collection, wherein health care data of the patients suffering from the cardio-cerebral vascular diseases is collected; 3 data preprocessing, wherein data integration, data cleaning, missing value processing, feature deleting and abnormal point removing are included; 4 feature engineering, wherein feature construction, feature selection and feature processing are included; 5 patient clustering modeling; 6 diagnosis and treatment scheme recommendation. Accordingly, an effective similarity analysis model for the patients suffering from the cardio-cerebral vascular diseases is built, a clinician can obtain the similar populations of a give patient through the patient features and then recommends a personalized treatment plan to achieve the purpose of accurate medical treatment, population grouping based on similarity analysis can be well conducted on the patients suffering from the cardio-cerebral vascular diseases in the Chinese population, and pointed personalized rehabilitation therapy is conducted on different risk populations as early as possible.