The invention discloses an X-ray differential phase contrast microscope system and a two-dimensional imaging method thereof. The X-ray differential phase contrast microscope system comprises a light source, a convergent lens, a center diaphragm, a beam splitting grating, a pin hole, a sample table, an object lens, an annular analysis grating and an imaging detector, wherein the light source is used for generating X rays; the convergent lens, the center diaphragm, the beam splitting grating, the pin hole, the sample table, the object lens, the annular analysis grating and the imaging detector are sequentially arranged in the X-ray spreading direction. The X-ray differential phase contrast microscope system has the beneficial effects that the X-ray differential phase contrast microscope system can realize the phase contrast quantitative imaging only through adding the beam splitting grating and the annular analysis grating in the conventional X-ray microscope; the advantages of simple structure and easy popularization are realized. In addition, the X-ray light source, the convergent lens and the beam splitting grating can be integrated into an X-ray annular grating source element; the length of the whole X-ray phase contrast microscope system can be further reduced; the manufacturing cost of the X-ray microscope system can be reduced; in addition, the light utilization efficiencyis further improved.