Although laminate structures are widely used in electrostatic capacitors, unavoidable heterogeneous interfaces often deteriorate the dielectric properties by impeding film crystallization. In this study, a TiO2/ZrO2/TiO2 (TZT) laminate structure, where upper-TiO2 deposited on the heterogeneous interface was crystallized by plasma-assisted atomic layer annealing (ALA), was investigated. ALA effectively induced the phase transition of the upper-TiO2 from the amorphous or anatase phase to the rutile phase, leading to an increase in the dielectric constant, whereas the ZrO2 blocking interlayer maintained the amorphous phase owing to the extremely localized effect of ALA. Consequently, through the layer-by-layer phase control of ALA, the dielectric constant of the upper-TiO2 was enhanced by 25% by applying ALA, leading to an increase in a capacitance density of 27% of the TZT capacitor, whereas a low leakage current density of ∼10-8 A/cm2 was maintained (at 1 V). In addition, the TZT capacitor on three-dimensional structures (aspect ratio of 5:1) shows a high capacitance density of up to 461 nF/mm2 owing to ALA.