SEBS block copolymers were treated under mild conditions in an ozone atmosphere, producing very slightly chemically-modified surfaces. The thermal stability was analysed by chemiluminescence and related to morphological changes observed by AFM. The intrinsic thermal stability was diminished by ozone exposure, but the oxidation induction times were delayed which indicates an enhancement of thermal stability under oxidative conditions. Also, chemiluminescence analysis showed the presence of a typical order–disorder transition at temperatures around 120 °C. Two different sets of samples which showed different morphological patterns were imaged by AFM. The effects of micro-domain separation and inter-domain structure on thermal properties are discussed and explained by a coarsening of the internal interface induced by ozone. A detailed 2D Fourier transformed analysis of AFM images allowed us to identify a regular wrinkled nano-pattern induced by uniaxial strain combined with ozone treatment, offering new opportunities in applications ranging from organic electronics to bio-patterning.