The importance of shale reservoir microstructure on field appraisal and flow mechanism has become increasingly prominent. But microscopic flow of shale reservoir cannot be studied effectively by conventional laboratory experiments and approaches for the unique characteristics of extra-low permeability，low porosity，serious anisotropy and heterogeneity. Digital core technology has become an important method in studying reservoir microstructure. Reconstruction methods have the accuracy and reliability. Shale core has been reconstructed by using traditional simulated annealing method based on the real shale SEM 2D images and data extracted by software. In order to solve the problem in reconstruction，an approach based on dual-region strategy and very fast simulated annealing（VFSA）algorithm is proposed in this paper. Using the new algorithm makes a significant improvement of computing efficiency. The shale is reconstructed in dual-region due to the pore distribution characteristics of shale. The results show that real pore distribution features are characterized better by this new approach.