This paper demonstrates that free-standing silicon nanocrystals (Si NCs) have significantly different thermal conductivity properties compared to Si NCs embedded in a host matrix. The temperatures of Si NCs under laser illumination have been determined by measuring the ratio of the Anti-Stokes to Stokes intensities of the first order Si–Si transverse optical (TO) phonon mode. It is found that large free-standing Si NCs are easily heated up to [similar]953 K by the laser light. The laser heating effects are reversible to a large extent, however the nature of the free-standing Si NCs is slightly modified after intensive illumination. The free-standing Si NCs can even be easily melted when exposed to a well-focused laser beam. Under these conditions, the blackbody radiation of the heated Si NCs starts to compete with the detected Raman signals. A simplified model of the heating effects is proposed to study the size dependence of the heated free-standing Si NCs with increasing laser power. It is concluded that the huge red-shift of the Si–Si TO mode observed under intensive laser illumination originates from laser-induced heating effects. In contrast, under similar illumination conditions Si NCs embedded in matrixes are hardly heated due to better thermal conductivity.