Structural effects in nanocrystalline pyrochlore Y2Ti2O7 induced by high energy heavy ions in a wide range of electronic stopping powers were studied by means of high-resolution transmission electron microscopy and molecular dynamics simulation considering the grain size effect. Ion track radii tend to saturate and even decrease at high electron stopping powers (>30 keV/nm) due to the velocity effect. The threshold electronic energy loss to form amorphous tracks in nanoclusters and large (>100 nm) crystals was estimated in the range 10.7–12.8 keV/nm. A strong size dependence was observed for smaller (<50 nm) isolated nanocrystals, with smaller crystals being significantly more sensitive to amorphous track formation.