The paper presents optical and thermal simulations of two kinds of thermally controlled silicon Photonic Crystal devices: an air hole in silicon slab that switches between two refractive behaviors, and a T-shaped circuit made by silicon rods in air that has an on-off behavior. Both effects have been obtained by increasing the device temperature, then exploiting the thermo-optic effect. Theoretical models of thermal dynamics, in particular for natural convective heat exchange on micrometric and sub-micrometric scale, have been validated by means of numerical simulations.