Enhancing molecular interaction is critical for improving the immobilization and stability of proteins on TiO2 surfaces. In this work, mesoporous TiO2 materials with varied pore geometries were decorated with phenyl phosphoric acid (PPA), followed by a thermal treatment to obtain chemically heterogeneous C-TiO2 samples without changing the geometry and crystalline structure, which can keep the advantages of both carbon and TiO2. The molecular interaction force between the protein and the surfaces was measured using atomic force microscopy by decomposing from the total adhesion forces, showing that the surface chemistry determines the interaction strength and depends on the amount of partial carbon coverage on the TiO2 surface (similar to 40-80%). Samples with 58.3% carbon coverage provide the strongest molecular interaction force, consistent with the observation from the detected friction force. Surface-enhanced Raman scattering and electrochemical biosensor measurements for these C-TiO2 materials were further conducted to illustrate their practical implications, implying their promising applications such as in protein detection and biosensing.