The thermal protection system (TPS) represents one of the most critical subsystems for vehicle re-entry. However, due to uncertainties in thermal loads, material properties, and manufacturing deviations, the thermal response of the TPS exhibits significant randomness, posing considerable challenges in engineering design and reliability assessment. Given that uncertain aerodynamic heating loads manifest as a stochastic field over time, conventional surrogate models, typically accepting scalar random variables as inputs, face limitations in modeling them. Consequently, this paper introduces an effective characterization approach utilizing proper orthogonal decomposition (POD) to represent the uncertainties of aerodynamic heating. The augmented snapshots matrix is used to reduce the dimension of the random field by the decoupling method of independently spatial and temporal bases. The random variables describing material properties and geometric thickness are also employed as inputs for probabilistic analyses. An uncoupled POD Gaussian process regression (UPOD-GPR) model is then established to achieve highly accurate solutions for transient heat conduction. The model takes random heat flux fields as inputs and thermal response fields as outputs. Using a typical multi-layer TPS and thermal structure as two examples, probabilistic analyses are conducted. The mean square relative error of a typical multi-layer TPS is less than 4%. For the thermal structure, the averaged absolute error of the radiation and insulation layer is less than 25 °C and 6 °C when the maximum reaches 1200 °C and 150 °C, respectively. This approach can provide accurate and rapid predictions of thermal responses for TPS and thermal structures throughout their entire operating time when furnished with input heat flux fields and structural parameters.