We report an unprecedented surface doping-driven anomaly in the compression behaviors of nanocrystals demonstrating that the change of surface chemistry can lead to an interior bulk structure change in nanoparticles. In the synchrotron-based X-ray diffraction experiments, titania nanocrystals with low concentration yttrium dopants at the surface are found to be less compressible than undoped titania nanocrystals. More surprisingly, an unexpected TiO2(ii) phase (α-PbO2 type) is induced and obvious anisotropy is observed in the compression of yttrium-doped TiO2, in sharp contrast to the compression behavior of undoped TiO2. In addition, the undoped brookite nanocrystals remain with the same structure up to 30 GPa, whereas the yttrium-doped brookite amorphizes above 20 GPa. The abnormal structural evolution observed in yttrium-doped TiO2 does not agree with the reported phase stability of nano titania polymorphs, thus suggesting that the physical properties of the interior of nanocrystals can be controlled by the surface, providing an unconventional and new degree of freedom in search for nanocrystals with novel tunable properties that can trigger applications in multiple areas of industry and provoke more related basic science research.