Upstanding SnO2 nanorod arrays covered by hierarchical SnO2 nanoflowers grow on the indium tin oxide (ITO) substrate through a direct hydrothermal method. Corresponding growth mechanism has been investigated along with the reaction time. The ITO substrate plays a role of seed layer and guides the nucleation of SnO2 nanoflower-rod arrays (NFRAs), which promotes the SnO2 crystal nucleation grow into nanorod arrays in the hydrothermal reaction. The photoluminescence (PL) spectrum of the obtained SnO2 NFRAs architecture reveals that the oxygen vacancies (V (O)) are major reasons of luminescence. In order to better understand the relationship between the V (O) and the luminous mechanism, a first principles study is carried out. The calculation results based on the density functional theory (DFT) indicate the energy level of V (O) with the three types of charge state (the ionization energy of the V (O) (0) state, V (O) (+) state, and V (O) (2+) state in band gap are 0.15, 2.84, and 3.15 eV, respectively) in SnO2 NFRAs architecture, which is in agreement with the PL spectrum.