The invention discloses a method and system for recording clinical scientific research data. The method and system aim at overcoming the defects that data used in clinical scientific research in the prior art is poor in reliability and can not meet the strict requirements in the aspects of facticity, integrity and the like. The recording method includes the steps that observation tables to be filled in are made for patients according to a database; follow-up visiting questionnaires made according to the observation tables are sent to the patients; the follow-up visiting questionnaires fed back by the patients and medical histories made by other hospitals and uploaded by the patients are received; other-hospital data of the patients is obtained from other hospitals; the medical histories and the other-hospital data are merged and subjected to duplicate removal processing, and scientific research data of other hospitals is obtained; the observation tables are filled in according to the scientific research data of other hospitals and the follow-up visiting questionnaires fed back by the patients. According to the method and system, the observation tables are generated based on unified standardization tables, continuous observation of a large number of samples can be achieved, the difficulty of clinical scientific researching is lowered, and the observed samples are enriched.