The thermal properties, including the heat capacity, thermal conductivity, effusivity, diffusivity, and phonon density of states of silicon-based nanomaterials are analyzed using a molecular dynamics calculation. These quantities are calculated in more detail for bulk silicon, porous silicon, and a silicon aerocrystal (aerogel), including the passivation of the porous internal surfaces with hydrogen, hydroxide, and oxygen ions. It is found that the heat capacity of these materials increases monotonically by up to 30% with an increase in the area of the porous inner surface and upon its passivation with these ions. This phenomenon is explained by a shift of the phonon density of states of the materials under study to the low-frequency region. In addition, it is shown that the thermal conductivity of the investigated materials depends on the degree of their porosity and can be changed significantly upon the passivation of their inner surface with different ions. It is demonstrated that, in the various simulated types of porous silicon, the thermal conductivity changes by 1–2 orders of magnitude compared with the value for bulk silicon. At the same time, it is found that the nature of the passivation of the internal nanosilicon surfaces affects the thermal conductivity. For example, the passivation of the surfaces with hydrogen does not significantly change this parameter, whereas a passivation with oxygen ions reduces it by a factor of two on average, and passivation with hydroxyl ions increases the thermal conductivity by a factor of 2–3. Similar trends are observed for the thermal effusivities and diffusivities of all the types of nanoporous silicon under passivation, but, in that case, the changes are weaker (by a factor of 1.5–2). The ways of tuning the thermal properties of the new nanostructured materials are outlined, which is important for their application.