In order to reduce the errors caused by the idealization of the conventional analytical model in the transient planar source (TPS) method, a finite element model that more closely represents the actual heat transfer process was constructed. The average error of the established model was controlled at below 1%, which was a significantly better result than for the analytical model, which had an average error of about 5%. Based on probabilistic optimization and heuristic optimization algorithms, an optimization model of the inverse heat transfer problem with partial thermal conductivity differential equation constraints was constructed. A Bayesian optimization algorithm with an adaptive initial population (BOAAIP) was proposed by analyzing the influencing factors of the Bayesian optimization algorithm upon inversion. The improved Bayesian optimization algorithm is not affected by the range and individuals of the initial population, and thus has better adaptability and stability. To further verify its superiority, the Bayesian optimization algorithm was compared with the genetic algorithm. The results show that the inversion accuracy of the two algorithms is around 3% when the thermal conductivity of the material is below 100 Wm−1K−1, and the calculation speed of the improved Bayesian optimization algorithm is three to four times faster than that of the genetic algorithm.