It has been shown that some block copolymers undergo a transition from a phase-mixed to phase-separated state, namely a lower disorder-to-order transition (LDOT) for block copolymers. These LDOT block copolymers can offer new types of sensor materials with high-temperatures or pressure sensitivities. In this paper, the characterization of the morphology from LDOT diblock copolymers such as polystyrene-b-poly(n-propyl methacrylate) and polystyrene-b-poly(2-ethyl hexyl acrylate), where PS blocks are perdeuterated using time-of-flight secondary ion mass spectrometry (TOF-SIMS), is reported. TOF-SIMS depth profiling was obtained for the lamellar morphology of deuterated copolymers which was found to orient parallel to the surface of the substrate. This preferential orientation resulted in a periodic variation in the composition of each block that continued throughout the copolymer film. This alternative orientation was also found in films with thicknesses of approximately 610 nm. Their depth profiles showed consistently regular alternative patterns with the same period because the size of the lamellar structure was determined by the total number of monomers in the copolymer chain. In order to investigate the effect of the sample-stage temperature on the copolymer depth profiling, TOF-SIMS depth profiles were performed at room temperature and low temperatures of −100 °C. Copyright © 2012 John Wiley & Sons, Ltd.