Scaffold biomaterials derived from silk fibroin have been widely used in tissue engineering. However, mimicking the nanofibrous structures of the extracellular matrix (ECM) for achieving better biocompatibility remains a challenge. Here, we design a mild self-assembly approach to prepare nanofibrous scaffolds from silk fibroin solution. Silk nanofibers were self-assembled by slowly concentrating process in aqueous solution without any cross-linker or toxic solvent and then were further fabricated into porous scaffolds with pore size of about 200-250μm through lyophilization, mimicking nano and micro structures of ECM. Gradient water/methanol annealing treatments were used to control the secondary structures, mechanical properties, and degradation behaviors of the scaffolds, which would be critical for different tissue regeneration applications. With salt-leached silk scaffold as control, the ECM-mimetic scaffolds with different secondary structures were used to culture the amniotic fluid-derived stem cells in vitro to confirm their biocompatibility. All the ECM-mimetic scaffolds with different secondary structures represented better cell growth and proliferation compared to the salt-leached scaffold, confirming the critical influence of ECM-mimetic structure on biocompatibility. Although further studies such as cell differentiation behaviours are still necessary for clarifying the influence of microstructures and secondary conformational compositions, our study provides promising scaffold candidate that is suitable for different tissue regenerations.