In the present study, the effect of liquid filling of the nanopore network on thermal transport in porous Si layers was investigated by μ-Raman spectroscopy. The values of thermal conductivity of porous Si and porous Si-hexadecane composites were estimated by fitting the experimentally measured photoinduced temperature rise with finite element method simulations. As a result, filling the pores with hexadecane led to (i) an increase in the thermal conductivity of the porous Si-hexadecane composite in a wide range of porosity levels (40–80%) and (ii) a suppression of the characteristic laser-induced phase transition of Si from cubic to hexagonal form.