In the paper, we study the formation of laser-induced periodic surface structures (LIPSS) on diamond-like nanocomposite (DLN) a-C:H:Si:O films during nanoscale ablation processing at low fluences – below the single-pulse graphitization and spallation thresholds—using an IR fs-laser (wavelength 1030 nm, pulse duration 320 fs, pulse repetition rate 100 kHz, scanning beam velocity 0.04–0.08 m/s). The studies are focused on microscopic analysis of the nanostructured DLN film surface at different stages of LIPSS formation and numerical modeling of surface plasmon polaritons in a thin graphitized surface layer. Important findings are concerned with (i) sub-threshold fabrication of high spatial frequency LIPSS (HSFL) and low spatial frequency LIPSS (LSFL) under negligible surface graphitization of hard DLN films, (ii) transition from the HSFL (periods of 140 ± 30 and 230 ± 40 nm) to LSFL (period of 830–900 nm) within a narrow fluence range of 0.21–0.32 J/cm2, (iii) visualization of equi-field lines by ablated nanoparticles at an initial stage of the LIPSS formation, providing proof of larger electric fields in the valleys and weaker fields at the ridges of a growing surface grating, (iv) influence of the thickness of a laser-excited glassy carbon (GC) layer on the period of surface plasmon polaritons excited in a three-layer system “air/GC layer/DLN film.”