An extended depth of field microscope system for phase object detection includes an imaging optical module and a phase/intensity converting module. The imaging optical module has an object lens group, in which an axial symmetric phase coding is added, to produce an axial symmetric spherical aberration. A point spread function (PSF) and an image with extended depth of field can be obtained with a predetermined level of similarity. The phase/intensity converting module converts the phase change of the light passing the phase object, into an image light with change of light intensity.