Strontium (Sr) doped hydroxyapatite (HA) has been widely used in diverse biological applications. In this work, hydrothermal synthesis method was used to prepare HA and Sr doped HA nanoparticles. A series of experimental methods and the simulation method based on density functional theory (DFT) were used to investigate the effect of Sr doping on chemical composition, crystallinity, lattice parameters, morphology, and formation energies of HA. The experimental results indicated that the lattice parameters and crystal size of Sr doped HA nanoparticles increased. The crystallinity of Sr doped HA nanoparticles did not change significantly with the increasing concentration of Sr ions. The lattice parameters obtained by the simulation method were in good agreement with the experimental results. The formation energies indicated that Sr ion doping endowed the structure more stable, which also illustrated that the Ca(1) site was the preferential site for Sr doping at 10at% and mixed doping was a more preferred doping mode at 50at%.