The effects of desalted duck egg white peptides (DPs), phosphorylated DPs (PDPs) and DPs–calcium complexes (DPs-Ca) on calcium absorption in vivo were investigated. Ninety fast-growing male rats were divided into 10 groups and treated with different dosages of CaCO3, calcium gluconate, DPs-Ca as well as CPPs, DPs and PDPs supplemented with CaCO3. Eight-week oral administration results indicated that the high dosage PDPs+CaCO3 group was significantly higher than the high dosage DPs+CaCO3 group in calcium absorption, bone calcium content, BMD and maximum stress, but lower in ALP activity (P < 0.05). Additionally, the high dosage DPs-Ca group showed higher bone indices than the high dosage DPs+CaCO3, calcium gluconate and CaCO3 groups (P < 0.05). These results suggest that in vivo, phosphorylated DPs are more effective than DPs in improving calcium absorption and bone strength, and DPs–calcium complexes are more beneficial to bone tissues than the DPs and CaCO3 mixture.