An X-ray phase-shift contrast imaging method and the system thereof are provided. The X-ray phase-shift contrast imaging method utilizes characteristic X-rays of high throughput irradiating at the target from different positions or with different focal positions so as to form different X-ray images. The X-ray images are compared to define the voxels and combined to obtain a 3-D X-ray image. By using X-ray phase-shift contrast for imaging the soft tissue, the level of the image contrast may be enhanced several orders of magnitude and the linear energy transfer of the high energy photon beam is greatly reduced. Hence, the radiation dose absorbed by the tissue may be greatly reduced.
