Hydroxyapatite (HA) microsphere with abundant ordered mesoporous and large hollow structure was prepared at hydrothermal condition with the aid of citrate. The obtained microsphere was performed as a drug delivery carrier to evaluate its drug loading/releasing behaviour using alendronate (AL) as a model drug. Results revealed that HA particles performed high AL-loading capability (46.8wt % with respect to the powdered starting materials) and excellent AL-releasing behaviour (sustained drug releasing profile without burst release). Besides, although a proliferation inhibition phenomenon was observed as HA and AL-loading HA (HA-AL) co-cultured with mesenchymal stem cells (MSCs) at the initial stage, after prolonging co-culture period, compared with HA and control group, HA-AL promoted the cells' proliferation, meanwhile, it facilitated osteogenic differentiation of MSCs and enhanced the expression level of typical markers, all of that ensure HA microsphere is a promising carrier for bone repair.