The invention discloses a synchronous polarization phase shift focus measurement system based on a Linnik type interference microscope. The system comprises a white light source, a collimating mirror,a first quarter wave plate, a laser light source, a Kohler illumination system, a polarizing prism, a transflective mirror, a cubic beam splitting prism, two microscope objectives, a reference plane,a second quarter wave plate, an analyzer, a focusing lens, a beam splitting prism, an x-direction line array CCD and a y-direction line array CCD. The white light source generates white light, and plane polarized light is formed by means of collimation, polarization and the like. After being split by the cubic beam splitting prism, the light irradiates the reference plane and a tested sample through two microscope objectives. The return light is split by the beam splitting prism, and then irradiates the x-direction line array CCD and the y-direction line array CCD to generate an interference fringe image. Focus measurement is realized according to the defocus aberration change of the image. Laser is uniformly emitted by the Kohler illumination system, and is reflected by the polarizingprism and the like. The sample is directly written through the cubic beam splitting prism and the like. The system provided by the invention has the advantages of fast data processing and real-time focusing, and can acquire the position and shape information of the tested sample.