Understanding the interactions between porous materials and biosystems is of great important in biomedical and environmental sciences. Upon atomic force microscopy (AFM) adhesion measurement, a new experimental approach was presented here to determine the molecular interaction force between proteins and mesoporous TiO2 of various surface roughnesses. The interaction force between each protein molecule and the pure anatase TiO2 surface was characterized by fitting the adhesion and adsorption capacity per unit contact area, and it was found that the adhesion forces were approximately 0.86, 2.63, and 4.41 nN for lysozyme, myoglobin, and BSA, respectively. Moreover, we reported that the molecular interaction force was independent of the surface topography of the material but the protein type is a factor of the interaction. These experimental results on the molecular level provide helpful insights for stimulating model calculation and molecular simulation studies of protein interaction with surfaces.