The objective of this study was to explore the effect of combined magnetic fields (CMFs) on osteogenesis and the remodeling of newly formed bone at bone-tendon (BT) junction. Forty-eight mature rabbits in whom partial patellectomy was performed were used to establish a BT junction injury model at the patella-patellar tendon (PPT) complex and were then allocated to CMF treatment group (CMF group) or placebo treatment group (control group). Daily CMF therapy was delivered continuously from post-operative day 3 to weeks 4, 8, and 16. At each time point, the animals were sacrificed, and the PPT complexes were harvested for radiographic, histological, peripheral quantitative computed tomography, and micro-computed tomography (micro-CT) evaluation. The area, length, and bone mineral density of the newly formed bone in the CMF group were significantly greater than the control group at post-operative weeks 8 and 16. The micro-CT results showed that the newly formed bone in the CMF group contained more and thicker trabeculae than the control group at weeks 8 and 16. Histologically, the CMF group showed better remodeling of the BT junction. In conclusion, CMF treatment was able to accelerate osteogenesis during BT junction repair, thus facilitating the healing of BT junction injury.