The invention discloses a magnetic separation-based multi-sample multi-site high-flux nucleic acid analysis system which comprises four parts, namely an XYZ three-axis mechanical arm and control circuit, an accurate temperature control system worktable and control circuit, a high-flux fluorescence signal detection worktable and control circuit and system control software. According to the system, a porous plate serves as a reaction container, various function modules are contained to be matched with the system, various biochemical reactions in the nucleic acid detection process can be finished under coordination and control of the system control software, and the specific functions comprise accurate liquid transfer, accurate working plate transfer, rapid magnetic separation, automatic sucker installation and discard, accurate temperature control process, low-temperature sample storage, high-flux fluorescence signal detection and system software overall control. According to the magnetic separation-based multi-sample multi-site high-flux nucleic acid analysis system, a magnetic separation technology, a particle microarray technology, a single base extension technology and an automation system are combined, and a novel high-flux nucleic acid detection system is established on the basis of a series of novel high-flux, automatic, high-specificity and high-practicality single base difference detection methods.