The purpose of this study was to evaluate the glucose cross-linked gelatin/zein scaffolds for bone regeneration in vitro and in vivo. The nanofibrous scaffolds exhibited fast mineralization in the concentrated simulated body fluid with the deposited octacalcium phosphate and dicalcium phosphate dehydrate. The nanofibrous scaffolds exhibited no cytotoxic effect on MC3T3e1 cells in a CCK-8 test. Additionally, scanning electron microscope and confocal laser scanning microscopy images revealed that all the scaffolds were biocompatible and showed excellent support for MC3T3e1 cells. In the osteogenesis characterizations, Alizarin Red staining experiments indicated the improved calcium deposits on the cross-linked scaffolds, while the alkaline phosphatase activity showed no difference. Furthermore, the in vivo cranial bone regeneration results suggested that the cross-linked gelatin/zein scaffolds presented a strong positive effect on the cranial bone regeneration with the increased new bone volume and connective tissue formation, but the incorporation of zein in the gelatin scaffolds did not favor the bone regeneration. Moreover, the cross-linked gelatin scaffold retarded the bone resorption as indicated by the higher levels of IFN-γ and lower levels of IL-6, which restricted the differentiation of osteoclasts.