Ablation of the thermal protection material of the reentry hypersonic flight vehicle is a complex physical and chemical process. To estimate the surface heat flux from internal temperature measurement is much more complex than the conventional inverse heat conduction problem case. In the paper, by utilizing a two-layer pyrogeneration-plane ablation model to model the ablation and charring of the material, modifying the finite control volume method to suit for the numerical simulation of the heat conduction equation with variable-geometry, the CGM along with the associated adjoint problem is developed to estimate the surface heat flux. This estimation method is verified with a numerical example at first, the results show that the estimation method is feasible and robust. The larger is the measurement noise, the greater is the deviation of the estimated result from the exact value, and the measurement noise of ablated surface position has a significant and more direct influence on the estimated result of surface heat flux. Furthermore, the estimation method is used to analyze the experimental data of ablation of blunt Carbon-phenolic material Narmco4028 in an arc-heater. It is shown that the estimated surface heat flux agrees with the heating power value of the arc-heater, and the estimation method is basically effective and potential to treat the engineering heat conduction problem with ablation.