One of the latest trends in the regenerative medicine is the development of 3D-printing hydrogel scaffolds with biomimetic structures for tissue regeneration and organ reconstruction. However, it has been practically difficult to achieve a highly biomimetic hydrogel scaffolds with proper mechanical properties matching the natural tissue. Here, bacterial cellulose nanofibers (BCNFs) were applied to improve the structural resolution and enhance mechanical properties of silk fibroin (SF)/gelatin composite hydrogel scaffolds. The SF-based hydrogel scaffolds with hierarchical pores were fabricated via 3D-printing followed by lyophilization. Results showed that the tensile strength of printed sample increased significantly with the addition of BCNFs in the bioink. Large pores and micropores in the scaffolds were achieved by designing printing pattern and lyophilization after extrusion. The pores ranging from 10 to 20 μm inside the printed filaments served as host for cellular infiltration, while the pores with a diameter from 300 to 600 μm circled by printed filaments ensured sufficient nutrient supply. These 3D-printed composite scaffolds with remarkable mechanical properties and hierarchical pore structures are promising for further tissue engineering applications.