In an attempt to fabricate biomimetic bone repair scaffolds and improve bone regeneration point of view, we have three dimensionally printed porous scaffolds with biomineralized hydroxyapatite/silk fibroin nanocomposites. SF/HA composite particles were firstly produced via an in-situ mineral precipitation process when SF molecules were served as templates.. Microscopy observations of SF/HA showed homogeneous morphology and narrowly distributed size. By using sodium alginate (SA) as paste binder, scaffolds with different contents of SF/HA were subsequently 3D-printed under proper conditions. All the scaffolds were porous with 3D interconnected large pores (size ～400 μm) and an overall porosity about 70%, combined with a relative high compressive strength (>6 MPa). The in vitro biological properties of degradation, apatite formation, human bone marrow-derived mesenchymal stem cells (hBMSCs) proliferation and differentiation were characterized on SF/HA-SA scaffolds. Results indicated that more apatite newly formed on the scaffold surface after soaking in SBF and original deposited HA minerals would recrystallize. In addition, the pH values of medium microenvironment remained steady in the range from 6.9 to 7.1 in one month. Cell attachment and penetration into scaffolds were supported by all the groups. Increased content of SF/HA led to better cell proliferation, and enhanced ALP activity as well. Bovine serum albumin (BSA) protein was selected as a model drug to be loaded into SF/HA-SA scaffolds in printing process, and the drugs released in a relative sustained manner in 5 days. These results suggest a promising application of SF/HA-SA scaffolds in bone regeneration.