This work explores a hydrothermal route to synthesis of self-doped SiO₂/SnO₂/SnO₂:Sn²⁺ nanostructures with controlled hierarchical structures and lattice parameters for tunable optical and photocatalytic properties. The effects of Sn²⁺ self-doping in the SnO₂ lattice on the local structure, electronic structure, and photodegradation of methyl orange were systematically investigated. It is found that two layers of SnO₂ and SnO₂:Sn²⁺ nanocrystals with thicknesses of 13 and 8 nm were coated on SiO₂ spheres showing monodispersed features. By Sn²⁺ doping, a blue shift of the Sn 3d XPS binding energy was observed, which is thought to be mainly related to the difference in electronegativity of Sn⁴⁺, Sn²⁺ and variation of lattice parameters. In contradiction to the quantum size effect, the self-doped SiO₂/SnO₂/SnO₂:Sn²⁺ nanostructures showed an abnormal red shift of band gap energy, which is related to doping effects and variations of lattice parameters. With well-defined lattice structure and electronic structure, the photocatalytic performance of SiO₂/SnO₂/SnO₂:Sn²⁺ nanostructures can be well regulated and optimized.