It was previously found that soybean protein hydrolysates (SPHs) can bind with calcium to form soluble complexes and promote calcium uptake by Caco-2 cells. However, the role of SPHs-calcium complexes on bone mass still needs to be explored. Fast growing male and female rats (n = 72) were assigned to eight groups: Control, lactic acid calcium (LCa), SPHs-calcium complexes (SPHCa) and casein phosphopeptides calcium (CPPCa). After four weeks treatment, oral administration of SPHCa significantly increased femur BMD of rats compared with Control and LCa groups (P < 0.05), while there are no obvious difference on the BMD of femur and lumbar vertebrae between SPHCa and CPPCa groups. Also, SPHCa showed a tendency to improve the mechanical properties of vertebra lumber for female rats. These findings suggest that the SPHs-calcium complexes might have positive effects on bone accretion of fast growing animals. This study brings new insight for better understanding the role of soybean protein itself on bone mass.