Abstract: The transition prediction of hypersonic boundary layer has been a difficulty in fluid dynamics. The friction coefficient and heat-transfer coefficient could be changed because of transition. The location of transition has an effect on thermal environment around the aircraft surface, which accounts for marked changes of Aeroelastic characteristics further. Considering the uncertainly of transition prediction of hypersonic boundary layer, this paper has analyzed the effects of transition location to aerothermodynamics of hypersonic all-movable control surface. First of all, the thermal environment around the control surface is obtained by solving the N-S (Navier-Stocks) equation using the model of laminar and turbulent flow respectively. In the next place, a parameterized model considering the given location of transition for temperature distribution is proposed. Base on this model, the structural thermal mode considering thermal stress and material inherent characteristics is analyzed. Finally the aeroelasticity is analyzed by the method of local flow piston theory based on CFD. This paper chooses an all-movable control surface as study subject with M=6, H=15 km and the calculation results show that:(1) As the transition location moving from leading edge to trailing edge, the structural frequencies increase and flutter velocity has an increased trend. Research indicates that maximum variation of flutter velocity is 6% brought by transition location; (2) When transition is located near the rudderpost, the flutter characteristics of the structure change violently. Decomposition and analysis of stiffness characteristic show that the major factor is the stiffness of rudderpost whose influence accounts for more than 80% of the whole structure.