The invention discloses an X-ray imaging system and method based on grating phase contrast and photon counting. X-rays become coherent X-rays after being shaped through a light source grating; the coherent X-rays containing phase changes after penetrating through samples form beam-split X-rays through a phase grating; the phase changes of the X-rays are converted into light intensity changes after the X-rays pass an analyzing grating; a photon counting detector is used for recording phase contrast information of the X-rays with different intensities; sectional images based on phase contrast are obtained through a three-dimensional reconstruction system; finally, components and interior fine structure information of the soft tissue samples are obtained. The system and method can be used for detecting soft tissue samples in the pathology department, the radiology department and the scientific research department of a hospital, early lesion information such as small lesions in the tissue samples can be found easily, and the detection rate is greatly increased.