The fundamental phase transition mechanism and the stability of the semiconductor-to-metal phase transition properties during multiple thermal cycles have been investigated on epitaxial vanadium dioxide (VO2) thin films via both ex situ heating and in situ heating by transmission electron microscopy (TEM). VO2 thin films were deposited on c-cut sapphire substrates by pulsed laser deposition. Ex situ studies show the broadening of transition sharpness (ΔT) and the width of thermal hysteresis (ΔH) after 60 cycles. In situ TEM heating studies reveal that during thermal cycles, large strain was accumulated around the domain boundaries, which was correlated with the phase transition induced lattice constant change and the thermal expansion. It suggests that the degradation of domain boundary structures in the VO2 films not only caused the transition property reduction (e.g., the decrease in ΔT and ΔH) but also played an important role in preventing the film from fracture during thermal cycles.