The invention discloses a clinical data standardization system and a standardized data acquisition method. The system comprises a standardized data acquisition platform, a data inspection platform anda business system; the standardized data acquisition platform comprises an in-row standard configuration module, a follow-up visit plan configuration module, a scientific research metadata managementmodule, a scientific research case management module, a standardized maintenance module, an acquisition module, a service interface module and an eCRF management module. The data acquisition method comprises the following steps: enabling a doctor workstation to generate a service application form and service system data based on the content to be followed by a patient, performing data cleaning and conversion through a standardization pool, and automatically filling a disease library of the eCRF management module after standardization processing. Under the condition of fully fusing standard codes and service interfaces in the biomedical field at home and abroad, the background annotation is carried out on differentiated standards, the differentiated standards are integrated into a dictionary, different standard backgrounds are compiled, and then correction is carried out through an algorithm, so that errors are reduced, and the bias rate is reduced.