To better use the numerical manifold method (NMM) to simulate complex continuous and discontinuous deformation problems, for the flexibility of the choice of mathematical covers in the NMM, we adopt the finite element mesh to generate NMM mathematical covers so as to avoid the appearance of too-small manifold elements, and put forward an independent cover method, in which a single material domain is described as one manifold element. Different cover types are coupled in the simulations of the tensile and compressive concrete meso-scale models, as well as a rock slope model with complex structures. The corresponding mechanical deformation and failure processes are well reproduced by NMM simulations. The coupling use of different cover types makes the generated NMM simulation models more reasonable. The independent cover method decreases the complexity to construct NMM simulation models for discrete systems, and reduces the numbers of manifold elements and the contact numbers along discontinuity surfaces, which helps to improve the NMM computational efficiency.