The invention discloses a secondary radar information processing system based on CPU (Central Processing Unit) and GPU (Graphic Processing Unit). The information processing system comprises system hardware including a radio frequency signal acquisition module, a computer, a GPU computing card and a communication network and system software including an operation system, a communication middleware,radar signal processing software, radar data processing software and management software. The total flow of information processing comprises the steps of sampling a radar signal; processing a secondary radar signal; processing secondary radar data; inputting, outputting, processing and controlling all the processes. By adopting the system, hardware bases of the radar system are general, the functions and the performance are defined by the software, and the defects of traditional radar in extensibility, diversity and reliability are overcome; meanwhile, the advantages of flexibility in use, higher reliability, lower use cost, lower energy consumption, updatability, extensibility and the like are brought, and the use efficiency of the system is improved.