The rock mass can be assumed to be homogeneous material from the macroscopic view, but it is a heterogeneous material at a mesoscopic scale and its physico-mechanical properties are discontinuous in space. Therefore, it is necessary to research the generation and development of pre-peak micro cracks in rocks and frictional characteristics between post-peak mineral particles from macro-meso and multi-scale perspectives to know the substantive characteristics of rock failure and instability. This paper, based on the manifold cover concept, proposes a new discrete element numerical method (i.e. Manifold Particle Discrete) combining with the particle contact model, so as to introduce the concept of stress boundary. This method can be applied to the entire process of analyzing rock failure. By analyzing the manifold cover and ball particle model, this paper constitutes the ball unit cover function of three-dimensional manifold cover, establishes tetrahedron units, obtains the equilibrium equation and compatible equation of the MPD model. It also verifies the accuracy of the proposed numerical method and the feasibility of rock failure analysis through numerical examples.