Strontium (Sr) compounds have become increasingly popular in osteoporosis treatment. As a bone seeking element, 98% of Sr deposits in bone and teeth after oral ingestion. However, the quality of new bone after Sr deposition is yet to be extensively investigated. In this study, eight osteopenic goats were divided into two groups: Ca + 40Sr (five goats) and controls (three goats). Controls were fed with low calcium feeds. Ca phosphate was supplied at 100 mg/(kg day), and Sr phosphate at 40 mg/(kg day) in the Ca + 40Sr group. The newly formed bone at the outer cortical area of the femur with Sr deposition was identified from tetracycline labels, and the morphology and lattice structure of the crystals in these regions were investigated. Results showed that Sr concentrations of bone tissue significantly increased 144.37% for Sr administration without significant change in Ca concentration, and the ingested Sr mainly deposited in new bone. The crystal isolated from new bone exhibited the typical character of biological apatite as determined by Fourier transform infrared spectroscopy and selected-area electron diffraction. Transmission electron microscopy examination showed that a crystal with width of 8-10 nm grew along with the (002) lattice and aligned with the same direction in both groups. The elemental analysis of crystals showed that the ingested Sr deposited mainly in the bone matrix or was absorbed on the bone crystal surface, while only a limited amount of Sr replaced Ca in apatite crystals. Our findings showed that Sr administration at current dosages for prevention and treatment of osteoporosis might not change the bone crystal morphology and structure.