The invention discloses a microscopy device for a controlled high-speed chromatography phase position. The microscopy device comprises a two-dimension scanning system, a first 4f system, a sample, a second 4f system, a piezoelectric ceramic control reflecting mirror, an optical path difference, a second polarization splitting prism, a polarizing film and a CCD (charge coupled device), wherein the two-dimension scanning system, the first 4f system, the sample and the second 4f system are successively arranged along a sample light path; the piezoelectric ceramic control reflecting mirror is arranged on a reference light path, and the optical path difference is used for changing the sample light path and the reference light path; the second polarization splitting prism is used for enabling the sample light and the reference light to become a bundle; the polarizing film and the CCD are successively arranged along an emergent light path of the polarization splitting prism. The invention also discloses a microscopy method of the controlled high-speed chromatography phase position. The microscopy device provided by the invention has the advantages that the system stability is high, the controllability is strong, the economy is good, the complicated angle scanning is realized, and the speed of a chromatography phase position microscopy system is increased by more than 4 times.