High spatial frequency laser induced periodic surface structures (HSFLs) on silicon substrates are often developed on flat surfaces at low fluences near ablation threshold of 0.1 J/cm2, seldom on microstructures or microgrooves at relatively higher fluences above 1 J/cm2. This work aims to enrich the variety of HSFLs-containing hierarchical microstructures, by femtosecond laser (pulse duration: 457 fs, wavelength: 1045 nm, and repetition rate: 100 kHz) in liquids (water and acetone) at laser fluence of 1.7 J/cm2. The period of Si-HSFLs in the range of 110–200 nm is independent of the scanning speeds (0.1, 0.5, 1 and 2 mm/s), line intervals (5, 15 and 20 μm) of scanning lines and scanning directions (perpendicular or parallel to light polarization direction). It is interestingly found that besides normal HSFLs whose orientations are perpendicular to the direction of light polarization, both clockwise or anticlockwise randomly tilted HSFLs with a maximal deviation angle of 50° as compared to those of normal HSFLSs are found on the microstructures with height gradients. Raman spectra and SEM characterization jointly clarify that surface melting and nanocapillary waves play important roles in the formation of Si-HSFLs. The fact that no HSFLs are produced by laser ablation in air indicates that moderate melting facilitated with ultrafast liquid cooling is beneficial for the formation of HSFLs by LALs. On the basis of our findings and previous reports, a synergistic formation mechanism for HSFLs at high fluence was proposed and discussed, including thermal melting with the concomitance of ultrafast cooling in liquids, transformation of the molten layers into ripples and nanotips by surface plasmon polaritons (SPP) and second-harmonic generation (SHG), and modulation of Si-HSFLs direction by both nanocapillary waves and the localized electric field coming from the excited large Si particles.