The invention relates to a calculation method for evaluating the heat insulation performance of a complex multi-layer thermal protection structure, and the method comprises the steps: determining the initial parameters of the multi-layer thermal protection structure, including the number of layers, the thickness of each layer, the thermophysical parameters of each layer, such as the density, the heat conductivity coefficient, the specific heat capacity, the equation of a heat absorption heat source, and the change relational expression of the air gap thickness and the thermophysical parameters; establishing a differential equation set of the multi-layer thermal protection structure, giving a thermal boundary condition and an interlayer continuity condition, dividing units based on a finite element method, discretizing the differential equation set, calculating a thermal capacity matrix, a thermal conductivity coefficient matrix and a thermal load matrix, and establishing a matrix equation set; and solving the matrix equation set by adopting a Gaussian-Seidel method to obtain node temperature and outer wall surface temperature distribution of the multi-layer thermal protection structure. The heat transfer calculation model of the multi-layer thermal protection structure can be established, and the method is suitable for evaluating the thermal insulation performance of the multi-layer thermal protection structure in different complex thermal environments.