A photon count-based radiation imaging system. The invention also relates to a method of implementing X-ray imaging in said system, and to key apparatus of said system. In the system, an x-ray source directs x-rays at a sample on a scanning platform. When the x-rays pass through said sample, photons carrying information about characteristics of the material at various spatial positions are produced. A photon count detector counts the photons on an imaging plane, obtains incident photon projection data and energy data, and transmits same to a 3D reconstruction system. The 3D reconstruction system reconstructs, on the basis of said projection data and energy data, the 3D structure and the matter composition inside the sample, then performs digital dyeing on the component parts of the sample, thereby differentiating the matter composition of the sample.