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.