Nanofiber microspheres are widely used in biomedical devices and tissue engineering for their unique structure and nanoscale effects but suffer from complex fabrication and limited biocompatibility. This study prepared hydrogel microspheres (specific surface area: 153.69 m2/g) via electrostatic spraying, using silk nanofibers (SNF) and sodium alginate (SA). These microspheres showed excellent biocompatibility (over 90% viability of human umbilical vein endothelial cells after 7 days of culture). As drug carriers, doxorubicin hydrochloride-loaded ones achieved 60% drug release within 72 h and reduced cancer cell viability to below 40%. Fluorescent peptide-grafted SNF/SA microspheres enhanced protease detection sensitivity (detection limit: 9.75 pM), outperforming conventional probes. Moreover, SNF/SA/hydroxyapatite (HAp) hybrid microspheres (with a hierarchically porous structure) promoted deep cellular migration in 7 days, increased osteoblast differentiation by over 50%, and accelerated proliferation by 30%, offering dual osteogenic activity and biocompatibility. This study provides an innovative strategy for silk fibroin-based biomedical devices and materials.