In the numerical simulations of highly fractured geological formations, discrete approaches are considerably promising and adequate to describe fluid flow in detail. However, the computational complexity increases dramatically with a greater number of fractures. This becomes the primary limitation for field-scale applications. In this study, a correlation index is for the first time introduced to evaluate the significance of individual fractures, and an equivalent model is proposed to mimic the original domain with a density-reduced one. By an equivalent permeability factor, the suggested model simplifies computational complexity, but compromises result precision to minor extent. This approach is validated in typical discrete fracture networks generated with stochastic fractal models. Effects of fracture geometry are discussed based on various distribution patterns. This method improves mesh quality when dealing with a fracture-matrix domain. It is also capable of optimizing reservoir design through fast and accurate estimations of gas productivity under different boundary conditions.