© 2018 Elsevier Ltd and Techna Group S.r.l. This study presents a new strategy for preparing highly oriented nanorod array of divalent ion substituted hydroxyapatite (HAp) and factors controlling the rate of glass conversion. HAp nanorod arrays were prepared on a series of alkali/alkaline-earth silicate glasses in the Na2O–CaO–SrO–SiO2 system in phosphate aqueous solutions with different pH values via a glass conversion process. The effects of the substitution of Sr2+ for Ca2+ and the network connectivity (NC) of the silicate glasses on the degree of crystal orientation of the nanorod array of HAp crystals, the crystallite size, and the partial substitution of Sr2+ for Ca2+ in the HAp crystal lattice were investigated using X-ray diffraction, 29Si magic angle spinning nuclear magnetic resonance (NMR) spectroscopy, and field-emission scanning electron microscopy. Sr-free Na2O–CaO–SiO2 glass was converted into HAp nanorod arrays highly-oriented toward the c-axis, whereas the increase in the NC of the glass led to a decrease in the rate of the conversion process from glass to HAp, which resulted in the reduction of the degree of c-axis orientation of the nanorod array of the HAp crystals. However, the rate of the conversion process was remarkably promoted in alkaline phosphate solutions, resulting in an increase of the degree of c-axis orientation of the nanorod array. The Sr/(Sr + Ca) molar fraction of silicate glasses determined the molar fraction of substituted Sr2+ in HAp crystal lattice.