A main challenge for use of scaffolds in bone engineering involves non-invasive monitoring in vivo and enhanced bone regeneration. The tissue-repair effect of super-paramagnetic iron oxide nanoparticles (SPIONs) was demonstrated previously by our group. However, testing in vivo is needed to confirm in vitro results. Here, SPIONs loaded gelatin sponge (GS) was used as a scaffold (SPIONs-GS) and implanted in the incisor sockets of Sprague-Dawley rats. Incisor sockets filled with nothing and filled with GS served as controls. Rats were sacrificed at 2 and 4 weeks. A significant decrease in the signal intensity of T2-weighted magnetic resonance imaging in the SPIONs-GS group was noted. Changes in image intensity of scaffolds (indicating scaffold degradation and interaction with host tissues) could be visually monitored over time. Micro-computed tomography showed that the SPIONs-GS group had more newly-formed bone (64.44±10.92 vs. 28.1±4.49, p < 0.0001) and a better-preserved alveolar ridge than blank control group at 4 weeks (0.962±0.01 vs. 0.92±0.01, p < 0.0001). Histology confirmed imaging results, showing good consistency in new bone formation and scaffold degradation. The number of SPIONs decreased rapidly with time due to quick degradation of GS, whereas the number of endocytic SPIONs in cells increased with time. These residual SPIONs, together with newly-formed bone, could be detected by MRI at 4 weeks. Therefore, it was clear that SPIONs induced active osteogenesis. In conclusion, good visibility on MRI and enhanced regeneration of bone can be obtained by implanting SPIONs-GS in vivo without using an external magnetic field.