The cytocompatibility of titanium oxides (TiO2) and oxynitrides (N-TiO2, TiOxNy) thin films depends heavily on the surface topography. Considering that the initial relief of the substrate and the coating are summed up in the final topography of the surface, it can be expected that the same sputtering modes result in different surface topography if the substrate differs. Here, we investigated the problem by examining 16 groups of samples differing in surface topography; 8 of them were hand-abraded and 8 were machine-polished. Magnetron sputtering was performed in a reaction gas medium with various N2:O2 ratios and bias voltages. Abraded and polished uncoated samples served as controls. The surfaces were studied using atomic force microscopy (AFM). The cytocompatibility of coatings was evaluated in terms of cytotoxicity, adhesion, viability, and NO production. It has been shown that the cytocompatibility of thin films largely depends on the surface nanostructure. Both excessively low and excessively high density of peaks, high and low kurtosis of height distribution (Sku), and low rates of mean summit curvature (Ssc) have a negative effect. Optimal cytocompatibility was demonstrated by abraded surface with a TiOxNy thin film sputtered at N2:O2 = 1:1 and Ub = 0 V. The nanopeaks of this surface had a maximum height, a density of about 0.5 per 1 µm2, Sku from 4 to 5, and an Ssc greater than 0.6. We believe that the excessive sharpness of surface nanostructures formed during magnetron sputtering of TiO2 and N-TiO2 films, especially at a high density of these structures, prevents both adhesion of endothelial cells, and their further proliferation and functioning. This effect is apparently due to damage to the cell membrane. At low height, kurtosis, and peak density, the main factor affecting the cell/surface interface is inefficient cell adhesion.