The interfacial contact status of a joint determines the sealing performance of an aircraft hydraulic system, which is influenced by inevitable multiscale assembly errors and joint manufacturing deviations. To address these challenges, a novel geometric analysis model was heuristically created that incorporates assembly and manufacturing-related topographies to accurately estimate the initial relative assembly position of joint surfaces. A microscopic contact model was constructed using the reverse reconstruction approach based on measured surface characteristics. Combining the relative position, a multiscale finite element contact model was generated to investigate the impact of each scale topography on the contact state of the seal ring. The experimental data verified the simulated indentation findings, confirming the model's efficacy in estimating contact status and seal performance characteristics. It is found that the flare angle has a more obvious effect on the contact state of the sealing interface, and a 2° difference in angle under the same load can cause a 28.19% difference in contact area, which greatly affects the sealing performance.