With the fast development of hypersonic aircrafts, the traditional passive thermal protection system (TPS) can't a ord the increasing demand of the thermal protection for aircrafts and engines. As a result, the actively cooling TPS has received more and more attentions. The commonly used technologies do require a substantially much more time due to the complexity of the structures. In this paper, the integrated unit method is proposed for solving spatially periodical structural problems using the boundary element method (BEM) and it is used to solve the thermal and mechanical problems appearing in the TPS with actively cooling channels. In this method, the BEM cell equation only needs to be established for one computational cell and the integrated unit can be formed by a specified number of cell equations. The equations of final system can be formed by the integrated unit equations. The proposed integrated unit method inherits the variableelimination idea of the sub-structure technique and assimilates the easy assembling characteristic of the conventional finite and boundary elements, and therefore is suitable for fast analysis of large-scale spatially periodical structural problems. As the coefficient matrices of the integrated unit only needs to be established once and the equations of final system only includes boundary nodal variables, the computational efficiency can be improved considerably. Three numerical examples for actively cooling combustors of scramjet engine are given to demonstrate the computational accuracy and efficiency of the proposed method.