This work analyses the three-dimensional (3-D) surface texture of carbon–nickel (C–Ni) films grown by radio frequency (RF) magnetron co-sputtering on glass substrates. The C–Ni thin films were deposited under different deposition times, from 50 to 600 s, at room temperature. Atomic force microscopy was employed to characterize the 3-D surface texture data in connection with the statistical, and fractal analyses. It has been found that up to 180 s the sputtering occurs in more metal content mode and in greater than 180 s it occurs in more non-metal content mode. This behavior demonstrated a strong link between the structural and morphological properties of C–Ni composite films and facilitates a deeper understanding of structure/property relationships and surface defects in prepared samples. Furthermore, these findings can be applied to research on the mechanisms to prepare and control high-quality C–Ni films.