Based on basic theory of numerical manifold method, effects of cover displacement functions for the stiffness matrix is analyzed with the relationship between the cover displacement function and the formation of the stiffness matrix. The increasing speed of matrix element value has relation to the values of absolute coordinates in cover displacement function. An improved function is adopted for better solution to solve partial oversize problem of stiffness values in the stiffness matrix with the highorder cover displacement function. The validity of the proposed approach is approved with case study.