The integration of bottom-up fabrication techniques and top-down methods can overcome current limits in nanofabrication. For such integration, we propose a gradient area-selective deposition using atomic layer deposition to overcome the inherent limitation of 3D nanofabrication and demonstrate the applicability of the proposed method toward large-scale production of materials. Cp(CH₃)₅Ti(OMe)₃ is used as a molecular surface inhibitor to prevent the growth of TiO₂ film in the next atomic layer deposition process. Cp(CH₃)₅Ti(OMe)₃ adsorption was controlled gradually in a 3D nanoscale hole to achieve gradient TiO₂ growth. This resulted in the formation of perfectly seamless TiO₂ films with a high-aspect-ratio hole structure. The experimental results were consistent with theoretical calculations based on density functional theory, Monte Carlo simulation, and the Johnson-Mehl-Avrami-Kolmogorov model. Since the gradient area-selective deposition TiO₂ film formation is based on the fundamentals of molecular chemical and physical behaviours, this approach can be applied to other material systems in atomic layer deposition.