Nanofibrous scaffolds mimicking important features of the native extracellular matrix (ECM) provide a promising strategy for tissue regeneration. However, 3D scaffolds mimicking natural protein nanofibers and bioactive glycosaminoglycans remain poorly developed. In this study, a biomimetic nanofibrous scaffold composed of natural silk protein nanofibers and glycosaminoglycan hyaluronic acid (HA) was developed. HA functionalization significantly improved the hydrophilicity and bioactivity of silk nanofibers (SNFs). SNFs can be assembled into nanofibrous aerogel scaffolds with low density and desirable shapes on a large scale. More importantly, with the assistance of HA, the silk nanofibrous aerogel scaffolds with ultra-high porosity, natural bioactivity, and structural stability in aqueous environment can be fabricated. In the protease/hyaluronidase solution, the SNF scaffolds with 10.0 % HA can maintain their monolithic shape for >3 weeks. The silk nanofibrous scaffolds not only imitate the composition of ECM but also mimic the hierarchical structure of ECM, providing a favorable microenvironment for cell adhesion and proliferation. These results indicate that this structurally and functionally biomimetic system is a promising tissue engineering scaffold.