For the supercritical n-decane horizontally flowing in a rectangular channel of an active regenerative cooling system, a transient thermal–fluid–structure coupling method is employed to investigate the unsteady thermal-hydraulic characteristics and the wall deformation at a starting stage. The temperature distributions of the fluid domain and solid domain along the flow direction are investigated at fixed times as well as at a certain cross section. Streamlines in cross sections are employed to explain the temperature distribution. The velocity and pressure at a fixed point versus time are also given. Besides, the solid deformation is presented according to the uneven pressure distribution and temperature distribution. It is found that the response time is less than 30 s when the heat flux is less than 3.0 MW/m2. A larger heat flux contributes to promoting the steady state. The high-temperature part of the solid domain is close to the heated wall, but the situation is reversed for the fluid domain. This is because a bunch of dead-zone vortices appears in the vicinity of the upper wall of the channel. The maximum deformation is 0.132 mm for the condition of heat flux 3.0 MW/m2 and it is exacerbated by the uneven temperature and pressure distributions on the solid domain.