Burn injuries have been reported to be an important cause of morbidity and mortality and they are still considered as unmet clinical need. Although there is a myriad of effective stem cells that have been suggested for skin regeneration, there is no one ideal scaffold. The aim of this study was to develop a three-dimensional (3D) bi-layer scaffold made of biological decellularized human amniotic membrane (AM) with viscoelastic electrospun nanofibrous silk fibroin (ESF) spun on top. The fabricated 3D bi-layer AM/ESF scaffold was submerged in ethanol to induce β -sheet transformation as well as to get a tightly coated and inseparable bi-layer. The biomechanical and biological properties of the 3D bi-layer AM/ESF scaffold were investigated. The results indicate significantly improved mechanical properties of the AM/ESF compared with the AM alone. Both the AM and AM/ESF possess a variety of suitable adhesion cells without detectable cytotoxicity against adipose tissue-derived mesenchymal stem cells (AT-MSCs). The AT-MSCs show increased expression of two main pro-angiogenesis factors, vascular endothelial growth factor and basic fibroblast growth factor, when cultured on the AM/ESF for 7 days, when comparing with AM alone. The results suggest that the AM/ESF scaffold with autologous AT-MSCs has excellent cell adhesion and proliferation along with production of growth factors which serves as a possible application in a clinical setting for skin regeneration.