In this paper, we take advantage of a facile fabrication technique called self-assembled nanosphere lithography (SANSL) combining with proper two-step reactive ion etching (RIE) method and radio frequency (RF) sputtering deposition process for manufacturing honeycomb diamond-like carbon (DLC) thin film structures with hydrophobic and high transparent properties. It is found that the DLC thin films deposited on clean glass substrates at the RF power of 100 W with the surface roughness (R
a) of 2.08 nm and the I
D/I
G ratio of 1.96 are realized. With a fill-factor of 0.691, the honeycomb DLC patterned thin film shows the best transmittance performance of 87% in the wavelength of visible light, and the optimized contact angle measurement is ∼108°. Compared with the pure DLC thin film and original glass substrate, the hydrophobic property of the patterned DLC films is significantly improved by 80 and 160%, respectively.