The numerical simulation of seepage in fractured porous media holds significant relevance for subsurface energy development. The presence of fractures at various scales profoundly influences the hydraulic properties of porous media during seepage. A peridynamic (PD)‐based frame is proposed for the seepage problem analysis of multiscale fractured porous media, in which micro‐fractures are implicitly represented like the porous media, macro‐fractures are explicitly represented. For fluid flow modeling, the peridynamic bonds are divided into three types: pore seepage bond, fracture seepage bond, and fluid exchange bond. The micro‐permeabilities of different bonds are derived by Darcy's law, Poiseuille's law, and fluid exchange model, respectively. The proposed peridynamic model can naturally simulate the seepage problem of porous rock with multiscale fractures in a unified framework. Then, four cases of pore seepage and fracture seepage are analyzed using the proposed model, fractured porous media seepage with micro‐fractures and macro‐fractures are respectively considered. The predicted results are compared with the available theoretical solutions, the close agreement shows that the wide validity and applicability of the proposed model in multiscale seepage problems.