This study presents a method for estimating the space-dependent thermal contact resistance between the two-layer walls of a furnace using the boundary element method (BEM) and conjugate gradient method (CGM) for the heat conduction problem. The global solution equation in matrix form is derived using the interface conditions, and the BEM is used to solve the direct problem. The CGM minimizes the objective function and calculates the sensitivity coefficients with the complex variable derivation method (CVDM). Comparative results show that the present approach is more accurate, stable, and efficient than the conventional CGM, which is attributed to the calculation of the sensitivity coefficients by CVDM. The effects of the value of thermal contact resistance, thermal conductivity ratio, Biot number, initial guess, measurement error, and the number and position of measurement points on the inversion results are also analyzed. Finally, the effectiveness of this approach is demonstrated through numerical examples, and the inversion results show its stability, efficiency, and accuracy in identifying different and complex distributions of thermal contact resistance. Furthermore, this approach is feasible for nonintrusive measurement, which is very meaningful in practical applications.