The invention provides a specific selective amplification and multiplex PCR method and application, and relates to the technical field of biology. The specific selective amplification and multiplex PCR method comprises the following steps: by taking endonuclease IV as mediation, identifying a base removal site and cutting a specific primer to obtain an extendable primer, and applying the extendable primer to PCR amplification; tHF is introduced in the middle of the specific primer to serve as a base removal site, sequences on the two sides of THF are complementary with a template, the 3'end is closed, and the specific primer is free of free hydroxyl and cannot extend. The multiplex PCR method provided by the invention can be used for performing multiplex PCR amplification on a biological genome, performing multiplex target amplification of amplicon library establishment, simultaneously detecting multiple pathogens, preparing a kit for simultaneously detecting multiple pathogens, and the like. The key problems of interference, non-specific extension and the like among multiple PCR primers are well solved, multiple detection is realized, the sensitivity is high, rapidness and convenience are realized, and batch detection of samples can be realized.