Based on the influence of fragment storage velocity on thermal protection structure of certain type high altitude high speed aircraft, an equivalence simulation method is proposed to replace thermal protection system (TPS) composite structure with single material structure. The simulation results show that 15 mm TPS thermal protection structure plate can be equivalent to 4.3 mm aluminum alloy plate, compared with the test results, and the error is 5.6%. There is an obvious hole expansion around the hole formed by the fragment penetrating the TPS plate. By comparing the simulation results with the experimental results, it is found that the errors of front aperture and back aperture are 2.9% and 2% respectively, and the limit velocity errors of the aluminum alloy and TPS composite structure are 2.3% and 1.4%. The method has a certain reference value for the design and optimization of thermal protection composite structure.