The invention provides a method for modeling and simulating a three-dimensional discrete element for shale pneumatic and hydraulic fracturing. The method includes the steps of (1) establishing a three-dimensional close packing model with specific elastic property and destructive property according to a conversion formula, and establishing an integrated isotropic random module through particle diameter normal distribution adjustment and random packing, (2) adjusting the diameter of particles according to given confining pressure, setting particle anisotropic ellipsoid parameters, moving the boundary of the models, adjusting the confining pressure to the given value, and finally connecting a particle solidification model to obtain an anisotropic shale model with specific confining pressure and mechanical property, (3) establishing a hydraulic pressure cavity model and a hydraulic pressure boundary model according to requirements, generating hydraulic pressure and stress waves through mutual extrusion of water particles, and simulating generation and development of hydraulic fractures. The method avoids human influences of a traditional method based on continuity mechanics, can simulate the processes of hydraulic pressure propagation and hydraulic fracturing more really, and achieves predication of shale pneumatic and hydraulic fracturing.