The invention relates to a medical data collection and analysis method, comprising the following steps of 1, uploading original data to a data platform; 2, converting the original data to data in an RDF (Resource Description Framework) format by using a semantic annotation algorithm based on a conditional random field in combination with a dependency grammar; 3, associating RDF data of a same patient in the data processed in step 2 through a data mining algorithm, and storing the RDF data into an Hbase database based on a distributed file system; 4, analyzing data in the Hbase database by using a statistical method and a machine learning method to obtain analysis conclusions; 5, organizing and classifying the analysis conclusions to construct a therapeutic scheme knowledge base. According to the medical data collection and analysis method and a system, the whole clinical diagnosis and treatment data of the patient are collected pertinently, a large number of data are analyzed to clinically diagnose in assistance, forecast disease and analyze the patient; the medical data collection and analysis method and the system can clinically help doctors to make an effective, exact and individualized therapeutic scheme.