Dual‐porosity simulation is one of the most used and efficient approaches in modeling fractured porous media. The performance of this approach is highly dependent on the accuracy of the definition of matrix‐fracture transfer shape factor. In this paper, a two‐step computational algorithm is developed to enhance the accuracy of the dual‐porosity method in modeling large‐scale deformable porous media, particularly in the transient stage when the conventional dual‐porosity models are associated with some errors. Moreover, in the proposed finite element method (FEM)‐based algorithm, the interaction between the fluid and solid phases is taken into account using a modified expression for the conventional shape factor. To this end, an extended relationship is derived to calculate the hydro‐mechanical shape factor for deformable saturated porous media. An appropriate unit cell along with the consistent boundary conditions is introduced, and the corresponding hydro‐mechanical shape factor is numerically evaluated for the unit cell at each time step. Finally, the calculated time‐varying shape factors are employed in a dual‐porosity framework to simulate various case studies and investigate the influence of different parameters, including the boundary conditions, the fracture to matrix permeability ratio, and the fracture compressibility coefficient on the hydraulic and hydro‐mechanical time‐varying shape factors. Numerical simulations are carried out by employing the proposed dual‐porosity algorithm through two general problems and the results are compared with the fine‐grid direct numerical simulation. The results are promising and show that the present algorithm effectively and efficiently increases the precision of the dual‐porosity method in modeling large‐scale deformable problems.