The invention discloses an off-axis scanning holographic three-dimensional target real-time joint transformation recognition system and method, and belongs to the technical field of optical scanning holographic three-dimensional object real-time recognition. The recognition system comprises a laser, a spatial filter, a first lens, a first beam splitter, a first reflective mirror, a second lens, a shutter, a second reflective mirror, a second beam splitter, a first objective table, a third lens, a first photoelectric detector, a computer, a third reflective mirror, a spatial light modulator, a fourth lens, a second objective table, a second photoelectric detector and a real-time display. The three-dimensional object information is recorded in an off-axis scanning holographic mode, a complex electrical signal processing unit in traditional optical scanning holography is omitted, the light path of the system is simplified, and the recognition efficiency of the three-dimensional target object of the system is improved. The three-dimensional object hologram is recognized through optical joint transformation, the problem of accurate positioning points in matching correlation filtering recognition does not exist, the structure is flexible, and correlation operation is easy to achieve.