Three-dimensional (3D) porous silk scaffolds with good biocompatibility and minimal immunogenicity, have promising applications in different tissue regenerations. However, a challenge remains to effectively fabricate their microstructures and mechanical properties to satisfy specific requirements of different tissues. In this study, silk scaffolds were fabricated to form extracellular matrix (ECM) mimetic nanofibrous architecture in a mild process. A slowly increasing concentration process was applied to regulate silk self-assembly into nanofibers in aqueous solution. Then glycerol was blended with the nanofiber solution and induced silk crystallization in lyophilization process, endowing freeze-dried scaffolds water-stability. The glycerol was leached from the scaffolds, leaving similar porous structure at a micrometer scale but different topographies at nanoscale. Compared to previous salt-leached and methanol annealed scaffolds, the present scaffolds showed lower β-sheet content, softer mechanical property, and improved cell growth and differentiation behaviors, implying their promising future as platforms for controlling stem cell fate and soft tissue regeneration.