A low impact docking system with advanced capabilities has been developing for future spacecrafts, and its main interface docking seal (MIDS) is both a critical component and a research topic of interest. It is a typical design for the MIDS that adopts the elastomer seal-on-seal structure made of silicone rubbers, and the atomic oxygen (AO) in space had been found to take great effects on the sealing performance by previous experimental studies, especially for the seal leak, seal adhesion, and compression set. Exposure to AO may cause obvious changes on the sealing surface of the MIDS, and some characteristic parameters of morphology are proposed to characterize the changes in this study, including of the porosity, roughness and radius of curvature. Both the leakage model and the adhesion model of the MIDS are further developed to predict the sealing performance considering AO effects, which had been confirmed by the application experiments. The experimental data are in good agreement with the calculation data. The effects of AO on the sealing performance are simulated and analyzed by the proposed prediction models. The results are beneficial to the developments of the MIDS and other space seals.