We report an ionic liquid (IL) assisted hydrothermal method to synthesize anatase TiO2 nanocrystals (NCs), in which TiCl4 was used as precursor, l-butyl-3-methylimidazolium chloride (bmim(+)Cl(-)) as IL, and F- or SO42- ions as phase transformation inhibitor. The surfactant-like nature of I L was found to play a key role in controlling the crystallization process via controlling the aggregation manner of the NCs. The fine-tuning abilities of the operating parameters of the bmim(+)Cl(-)/TiCl4/H2O system facilitated the controlling over the shape and size of TiO2 NCs. Phase-pure anatase monodisperse NCs with Various shape and size were controllably obtained. Moreover, the aggregation manners of anatase NCs were also studied, and it was demonstrated that the high concentration of HF or H2SO4 could result in aggregation of anatase NCs to form pseudo single crystals.