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This invention belongs to the field of oil and gas production enhancement and stimulation technology. It provides a FDEM simulation method and system for mineral-scale shale hydration-induced fracturing. The method includes the following steps: obtaining target reservoir stress, rock porosity, and permeability; preparing rock samples from the target stratigraphic layer and obtaining the mineral composition and content through X-ray diffraction experiments; constructing a polycrystalline geometric model of the minerals using random Voronoi mosaic technology; conducting core immersion hydration experiments to obtain the relationship between core water content and time; setting initial and boundary conditions for the model and establishing a numerical model of clay mineral hydration expansion-induced fracturing based on the finite discrete element method; and conducting numerical experiments on shale hydration-induced fracturing to obtain the micro-fracture propagation morphology induced by clay mineral hydration expansion. This invention considers the non-uniform mosaic distribution of multiple minerals in the reservoir rock, simulates the non-uniform stress distribution induced by clay mineral water absorption and expansion, and realizes numerical simulation of the mineral-scale shale hydration-induced fracturing process.