The precise control of nanomaterial microstructure at the atomic level relies on the comprehensive understanding of atomic structural transition during the fabrication process at the atomic level. The phase transition from protonated titanate to TiO2 is a prevalent route to synthesize low dimensional TiO2-based nanomaterials, which exhibit excellent photocatalytic, lithium-ion battery performances, while the detailed phase transition mechanism remains to be clarified due to lack of atomic-level in situ information. Herein, the atomic structural transitions from one-dimensional H2Ti3O7 (HT) to TiO2(B) and anatase TiO2 (TB and TA) nanocrystals were revealed through in situ environmental transmission electron microscopy, which exhibited a two-step phase transition at 200–600 °C. (I) H2Ti3O7 to TiO2(B) transition began via an indirect pathway at ∼200 °C: The HT (200) interlayer dehydration occurred firstly with lattice shrinkage; Then TB discretely nucleated at the dehydrated H2Ti3O7 nanotube wall with a crystallographic relationship of (200)HT∥(200)TB {[001]HT∥[001]TB}; At higher temperature, the separated nuclei grew up with defects and distorted crystal lattice among them, which then connected and jointed to a single crystalline TB nanotube by atomic rearrangement. (II) The further transition of TiO2(B) to anatase TiO2 occurred via a direct pathway above 400 °C: Scarce nucleation event of TA phase was observed, which generated within TB nanocrystal with a crystallographic relationship of (200)TB∥(002)TA {[001]TB∥[010]TA}. Once a TA nucleus formed, it grew up to a large crystal by consuming the neighbor TB nanocrystals. These findings may contribute to comprehensively understanding phase transition and precisely manipulating the atomic structure of one-dimensional TiO2 nanocrystals.