The thermal stability of the thin film morphology of two symmetric oxyethylene/oxybutylene block copolymers (E76B38 and E114B56) on mica and silicon was investigated via atomic force microscopy (AFM). It is found that morphological transition of EmBn thin films during melting is strongly dependent on the molecular weight of the diblock copolymers and their interaction with the substrate. For E76B38 on mica, a single-layered structure transforms into a double-layered structure upon melting, but the same polymer on silicon retains a single-layered structure after melting and spreads quickly to wet-out the silicon surface. Conversely a longer polymer, E114B56, has a thin film on mica that does not change much after melting of the crystalline E block. A mechanism was proposed to explain the relative stability of E76B38 and E114B56 thin films upon melting. Internal stress is produced during melting and can be released along two directions. The release along the vertical direction is restricted by the energy barrier related to the segregation strength, and the release along the horizontal direction is dependent on the mobility of block copolymer related to the interaction between the block copolymer and the substrate. Domain size affects the release rate of the internal stress along the horizontal direction and thus the thermal stability of EmBn thin films. Switching between horizontal and vertical releases can be realized by controlling the domain size of the thin films.