Hepatocyte growth factor (HGF) is a novel potential therapy for improving bone health in patients with type II diabetes and hypertension, but its effect on the bone molecular structure is not revealed yet. Here, X-ray absorption near edge structure (XANES) spectroscopy was used to explore the effects elicited by HGF on the bone chemical structure. This study assessed local calcium (Ca) and phosphorus (P) coordination of diabetic hypertensive rat bones, each with and without HGF treatment. Results revealed that HGF has significant effects on Ca and P coordination chemistry as confirmed by presence of more soluble phosphates in the HGT-treated groups. Data indicated that treated bones have a poorly developed phosphate structure as evidenced by drastic drop in post-edge shoulder in P L2,3-edge compared to diabetic hypertensive and diabetic control bone. Presence of soluble Ca and P, products of bone resorption, with HGF treatment suggests unbalanced bone resorption and formation.