Silicon is one of the most interesting candidates for plasmon-free surface-enhaced Raman scattering (SERS), because of its high-refractive index and thermal stability. However, here we demonstrate that the alleged thermal stability of silicon nanoshells irradiated by conventional Raman laser cannot be taken for granted. We investigated the opto-thermal behavior of SiO2/Si core/shell microbeads (Si-rex) irradiated with three common Raman laser sources (λ = 532, 633, 785 nm) under real working conditions. We obtained an experimental proof of the critical role played by bead size and aggregation in heat and light management, demonstrating that, in the case of strong opto-thermal coupling, the temperature can exceed that of the melting points of both core and shell components. In addition, we also show that weakly coupled beads can be utilized as stable substrates for plasmon-free SERS experiments.