The invention discloses an automatic extraction and detection method of a super-sensitive trace target substance. The method comprises the steps that a vessel to be detected is used for collecting a sample to be detected, magnetic beads subjected to coating treatment are added, and a stirring rod provided with a magnetic bead adsorption film in a sleeved mode is inserted into the sample to be detected in the vessel to be detected; by means of rotation of the stirring rod, the opportunity of specific adsorption between the added magnetic beads and the target substance in the sample to be detected is increased; by magnetizing the stirring rod to enable the stirring rod to attract the magnetic beads, antigens bonded with the magnetic beads conduct specific bonding with antibodies on the magnetic bead adsorption film; by conducting demagnetizing on the stirring rod and rotating the stirring rod, the magnetic beads which are not subjected to specific bonding are removed from the surface of the adsorption film; the magnetic beads adsorbed by the magnetic bead adsorption film of the stirring rod are eluted in eluent, and the extraction work is completed; the magnetic beads in the eluent are put into a magnetic detector to be detected, a difference between induction signal of a detection coil and a reference coil is compared, an induction signal change caused by intervention of a paramagnetic material for detecting the magnetic beads can be obtained, therefore, the quantity of biological signals marked by the magnetic beads is reported, and detection information is generated and reported.