To date, the feature size of microphase separation in block copolymers has been downsizing to 10 nm scale. However, morphological control for such a small feature is still a challenging task. The present Letter discusses a phase transition in a natural/synthetic "hybrid" block copolymer system based on an oligosaccharide and poly(ε-caprolactone) via thermal annealing. Time-resolved small-angle X-ray scattering investigation as a function of temperature indicated the phase transition from hexagonally close-packed cylinder to body-centered cubic at 10 nm scale. Atomic force microscope images of the block copolymer thin films annealed at different temperatures clearly confirmed the existence of these morphologies. The driving force of this phase transition (from cylinder to cubic) is the change of volume fraction of the block copolymer due to thermal caramelization.