In this paper we have carried out molecular dynamics simulation of the low-energy Ar ion irradiation of nanoporous homogeneous material with different porosity and pore sizes. Our results demonstrate that in a model with small pores (R-pore = 0.8 nm) and relatively low (22%) porosity, the pores at near-surface layers collapsed due to the ion bombardment, whereas in a model with larger pores (R-pore = 2.8 nm) and higher (44%) porosity no significant structural changes occurred under the same irradiation conditions. To study thermal stability of porous structures and to reveal the effects of both the pore radius and the porosity on pore collapsing, our nanoporous structures were subjected to gradual heating. The simulation results demonstrate distinct mechanisms of structural changes in the nanoporous materials depending on the value of the excess surface energy per unit volume.