Low cross-linking degree, weak mechanical strength, and poor osteoinductivity are significant obstacles in the development of bone repair materials. In this study, chitosan/gelatin/supersaturated calcium citrate scaffolds were prepared with the dehydrogenation heat treatment method. The results confirmed that citric acid significantly improved the cross-linking degree and efficiency of the chitosan/gelatin scaffolds. But the addition of Ca2+ reduced the cross-linking degree, water absorption, and resistance to enzymatic degradation of the scaffolds. While, the supersaturated calcium citrate formed inside the scaffold increased its mechanical strength. The biocompatibility and osteogenic activity of scaffolds were measured by inoculation with MC3T3-E1 cells. The rapid and efficient release of Ca2+ from the scaffolds could significantly promote cell adhesion, proliferation, and differentiation, while cell activities were inhibited by excessive Ca2+. The results of repairing skull defects in SD rats demonstrated that the chitosan/gelatin/supersaturated calcium citrate scaffolds with 25 mM Ca2+ added had a stronger osteogenic effect compared to the chitosan/gelatin scaffolds. Hence, the chitosan/gelatin/ supersaturated calcium citrate scaffolds prepared in this study are promising materials for treating bone defects. The appropriate amount of calcium salt added to the scaffold in order to optimize its biocompatibility and osteogenic activity deserves further investigation.