The development of high-power anode materials for Na-ion batteries is one of the primary obstacles due to the growing demands for their use in the smart grid. Despite the appealingly low cost and non-toxicity, Na2Ti3O7 suffers from low electrical conductivity and poor structural stability, which restricts its use in high-power applications. Viable approaches for overcoming these drawbacks reported to date are aliovalent doping and hydrogenation/hydrothermal treatments, both of which are closely intertwined with native defects. There is still a lack of knowledge, however, of the intrinsic defect chemistry of Na2Ti3O7, which impairs the rational design of high-power titanate anodes. Here, we report hybrid density functional theory calculations of the native defect chemistry of Na2Ti3O7. The defect calculations show that the insulating properties of Na2Ti3O7 arise from the Na and O Schottky disorder that act as major charge compensators. Under high-temperature hydrogenation treatment, these Schottky pairs of Na and O vacancies become dominant defects in Na2Ti3O7, triggering the spontaneous partial phase transition to Na2Ti6O13 and improving the electrical conductivity of the composite anode. Our findings provide an explanation on the interplay between intrinsic defects, structural phase transitions, and electrical conductivity, which can aid understanding of the properties of composite materials obtained from phase transitions.