The influence of thermal treatment on the structural features of mechano-synthesized fluorapatite–titania composite nanopowders was studied. A mixture of calcium and phosphate reagents was mixed with a certain amount of titania (20 wt%) and then was mechanically activated for 5 h, 10 h and 15 h respectively. After that, the mechano-synthesized powders were annealed at 700 ℃ for 2 h. The crystallite size of the composite nanopowders estimated from Williamson–Hall method was in good agreement with transmission electron microscopy (TEM) analysis. Scanning electron microscopy (SEM)/TEM images confirmed the formation of a cluster-like composite which was composed of ellipse-like nanoparticles with an average size of about 16±7 nm after 15 h of milling. During the milling process, large variations in mechanochemical behavior of the CaHPO₄–Ca(OH)₂–CaF₂–TiO₂ system were detected. After the beginning of milling, no trace of the composite was found due to the lack of sufficient time for the mechanical activation. When the mechanical activation time increased to 15 h, composite nanopowders with the crystallite size of around 21.66 nm were formed. During heating at 700 ℃, the recovery of crystallinity occurred and the fraction of crystalline phase reached a maximum around 88.79% for the 10-h milled sample. Results indicated that the structural features of the composite were strongly influenced by the subsequent annealing.