Efficient and accurate strength analysis of bolted connections is essential in analyzing the integral thermal protection system (ITPS) of hypersonic vehicles, since the system bears severe loads and structural failures usually occur at the connections. Investigations of composite mechanical properties used in ITPS are still in progress as the architecture of the composites is complex. A new method is proposed in this paper for strength analysis of bolted connections by investigating the elastic behavior and failure strength of three-dimensional C/C orthogonal composites used in ITPS. In this method a multi-scale finite element method incorporating the global–local method is established to ensure high efficiency in macro-scale and precision in meso-scale in analysis. Simulation results reveal that predictions of material properties show reasonable accuracy compared with test results. And the multi-scale method can analyze the strength of connections efficiently and accurately.