In this paper the theoretical model is built for ZEpHyR (ZARM Experimental Hybrid Rocket) main engine which is being developed at ZARM institute, Bremen, Germany. The theoretical model is used to estimate the temperature of exhaust gas. The Conjugate Gradient Method (CGM) with Adjoint Problem for Function Estimation iterative technique is used to solve the Inverse Heat Conduction Problem (IHCP) to estimate the heat flux and internal wall temperature at the throat section of the nozzle. Bartz equation is used to calculate the convective heat transfer coefficient. The exhaust gas temperature is determined using the estimated heat flux, the wall temperature at internal surface of nozzle and the heat transfer coefficient. The accuracy of CGM iterative scheme to solve the IHCP is also investigated and its results are presented.