The invention discloses a multi-source data assisted clinical decision support system and method. The system comprises a medical/pharmaceutical data storage unit, a clinical pathway/evidence storage unit, an information input unit, a comparison processor unit, a diagnosis and treatment result output unit and an early warning and operation recording unit. According to the multi-source data assisted clinical decision support system and method of the invention, feasible clinical diagnosis and treatment scheme suggestions and corresponding clinical research and real world research evidence support are provided for medical workers, the whole disease cycle of diagnosis, treatment, prognosis, out-of-hospital management, disease burden and the like is covered, and doctors are assisted to quickly improve the clinical diagnosis and treatment level; the contradiction that time and energy of medical workers are difficult to keep up with clinical research progress is solved, and medical resources are balanced. After the system is deployed to a hospital end, when a doctor makes a prescription, the system can carry out reasonable early warning on treatment and medication schemes specifically involved in a clinical path; based on individual differences of patients, the reasonability and safety of the medication schemes are ensured, and the overall medical service quality is improved.