The invention discloses an optical three-dimensional correlation identification device based on an integrated imaging system and an identification method. The device comprises a three-dimensional information acquisition device and a correlation identification system, wherein the three-dimensional information acquisition device comprises a sample rotation device, an optical microscope, a diffuse transmission element, a micro lens array, an imaging lens and a computer, the correlation identification system comprises a laser device, a first reflective mirror, a second reflective mirror, a reverse telescope system, a spatial light modulator, a first Fourier light transmission mirror, a third reflective mirror, a diaphragm, a light refractive crystal, a second Fourier light transmission mirror, a second CCD sensor and a spatial light modulator. The device has advantages of good amplification capability, high imaging quality, comprehensive three-dimensional information and excellent identification effect.