Natural monoclinic zirconia (baddeleyite) was irradiated with 340 MeV Au ions, and the irradiation-induced nanostructures (i.e., ion tracks and nanohillocks) were observed using transmission electron microscopy. The diameter of the nanohillocks was approximately 10 nm, which was similar to the maximum molten region size calculated using the analytical thermal spike model. Ion tracks were imaged as strained regions that maintained their crystalline structure. The cross-sections of most of the ion tracks were imaged as rectangular contrasts as large as 10 nm. These results strongly indicated that the molten region was recrystallized anisotropically, reflecting the lattice structure. Furthermore, low-density track cores were formed in the center of the ion tracks. The formation of low-density track cores can be attributed to the ejection of molten matter toward the surface. A comparison of the ion tracks in the synthetic zirconia nanoparticles and those in larger natural zirconia samples showed that the interface between the strained track contrast and the matrix was less clear in the former than in the latter. These findings suggest that the recrystallization process was affected by the size of the irradiated samples.