Safety and structural integrity of hypersonic vehicles are directly influenced by the reliability of their thermal protection system (TPS). To improve the efficiency of reliability analysis of TPS, a new method based on importance sampling was proposed in this paper. The detailed calculation procedure and thermal reliability assessment methods were also introduced. The thermal reliability analysis of a typical non-ablative TPS with uncertainties about material properties and geometries was used as numerical example to verify the effectiveness of the proposed method. The results indicate that to achieve reliability result with the same confidence level, importance sampling method needs only 10% simulation iterations of the conventional Monte Carlo method, which dramatically improves the efficiency of reliability analysis.