The present invention discloses a system and a method for complex brain disease targeted combination treatment analysis. According to the system and the method, a modern data mining technology, a complex network analysis technology, a cloud computing technology and a large data technology are effectively combined; potential drug targets of diseases are dynamically queried, analyzed and computed according to different brain diseases; and problems in current medical research are solved, such as long data processing time, a long research period, lack of systematicness, a single research target and the like. According to the system and the method, an authoritative medical database abroad is combined and disease treatment method research is enabled to be systematic, processed and normalized. Besides, according to the system and the method, cost of medical disease treatment analysis and research is also reduced, and application of an advanced computer technology in the medical field is expanded. The present invention aims to establish brand-new network pharmacology study method and technology, is of special significance to breakthrough in brain disease prevention and treatment research, and takes positive efforts and does contribution for supporting and leading research, development and industrialization of innovative drug in China.