Skin flap transplantations are common methods for covering and repairing tissue defects in surgery, while the survival rates of these skin flaps are still low due to the vascular crisis and necrosis. To improve this situation, herein a novel biohybrid scaffold is proposed by integrating the advantages of anisotropic fish scales and mesenchymal stem cells (MSCs) for skin flap regeneration. The fish scale scaffold is obtained through its decellularization and decalcification processes, which reserved intact collagen, glycosaminoglycan, and other endogenous growth factors for MSCs and human vascular endothelial cells proliferation. As the scaffold maintains intrinsic anisotropic structures on both surfaces, the proliferative cells can be elongated along the aligned structures on the fish scale, which endow them the capacity to differentiate into multiple directions. Based on these features, it is demonstrated from an in vivo experiment that the MSCs-loading fish scale scaffolds can effectively convert the activated inflammatory macrophages into anti-inflammatory properties, reduce the inflammation around the flap, and improve the survival rate. These results indicate that the MSCs-loading fish scale scaffold is suitable and has the potential for skin flap regeneration and functional recovery.