Interface stresses and sealing performance of thin-wall box-shaped bolted flanged joints using silicone sealant under internal pressure and thermal conduction conditions are analyzed by the thermo-elastic finite element method. The flexible flanges were fastened by M8 bolts and nuts with an initial clamping force (bolt preload) after being joined with the silicone sealant. In the elastic and thermo-elastic Finite Element Method (FEM) calculations, the effects of the bolt pitch distance, flange rigidity and flange thickness were examined on the interface stress distributions. In addition, the effects of the linear thermal expansion coefficient and Young's modulus of the silicone sealant in the steady temperature state were also examined from a design standpoint. In the experiments, leakage pressure was measured when the silicone sealant was applied between an aluminum flexible flange with 1 mm thickness and an aluminum flange (body) with 10 mm, thickness. Measurements of sealing performance with the silicone sealant and a sheet gasket were also conducted. In addition, strains in the joint in steady temperature states were also measured by strain gauges to understand the effect of the operative temperature on the sealing performance. The experimental results were found to be in fairly good agreement with the calculated results. From the results, it was found that the effect of the thermal conduction condition was greater than that of the internal pressure on both the interface stress distributions and the sealing performance. In addition, the sealing performance was found to be better in the joint with the silicone sealant than that with the sheet gasket.