This chapter covers the applications of computer simulations, including first-principles density functional theory calculations and molecular dynamics simulations, to the newly-born area of catalysis in the carbon nanotubes and metal oxide nanotubes. Nanotubes exhibit unusual mechanical, electronical and chemical properties unlike the bulk. Particularly, the transport, adsorption and chemical reactivities of molecules and nanomaterials confined inside nanotubes are different from those on the exterior walls of nanotubes. We mainly report our recent research progress in those extraordinary properties involved in nanotubes and the novel approaches to modulate the catalytic performances. Particular focus has also been devoted to the formation, structural and electronic properties of metal oxide nanotubes such as TiO2, ZnO and V2O5 nanotubes briefly. A short summary and outlook for computer simulations on catalysis in nanotubes is finally provided.