For improving the surface-enhanced Raman scattering (SERS) performance of nanomaterials to achieve trace detection of proteins and complex biological systems, structural and topographical control is one of the important strategies. In this work, a facial and effective method to optimize the topography of TiO2 nanotube arrays (TNAs) is demonstrated, together with a significant enhancement of the SERS performance of cytochrome C (Cyt C) on TNAs. An enhancement factor (EF) up to 104, which is obtained with the newly developed method on the basis of the quantification of atomic force microscopy (AFM)-measured interaction force, is achieved, corresponding to a superior detection limit of Cyt C down to 10-7 M. The main reason is that adjusting the fluoride contents in an electrolyte (from 0.4 to 0.1 wt %) can reduce the content and sizes of cracks, as well as the tube ruptures of TNAs, where the fluoride content at 0.2 wt % can successfully provide the excellent and optimized topography of TNAs. The TNAs with the optimized topography, especially those with larger tube diameters, demonstrated the importance of structural integrity on a remarkably excellent SERS performance in the trace detection of proteins. The proposed method will stimulate the development and optimization of the active substrate on the SERS applications in biology, bioanalysis, and nanoscience. © 2020 American Chemical Society.