We herein propose a novel way of producing nanofibrous gelatin–silica hybrid scaffolds through thermally induced phase-separation (TIPS) particularly using mixtures of gelatin solution and silica sol, which can mimic the physical structure, chemical composition, and eventually functions of the native bone extracellular matrix (ECM). The gelatin solutions were homogeneously hybridized with various contents of a silica sol using simple magnetic stirring, which enabled the construction of a nanofibrous structure with a uniform distribution of the silica in the gelatin nanofibers. The nanofibrous gelatin–silica hybrid scaffolds showed much better mechanical properties and in vitro biodegradation stability and apatite-forming ability than the nanofibrous pure gelatin scaffold, which were achieved by the presence of a stiff, bioactive silica phase in the nanofibers and the interaction between the silica hydroxyls and the amino group in the gelatin polymer. In addition, the nanofibrous gelatin–silica hybrid scaffold with a silica content of 30 wt% showed reasonably high in vitro biocompatibility. These findings suggest that the highly porous, nanofibrous hybrid structure mimicking the bone ECM can provide an excellent matrix for bone tissue regeneration.