High-low alternating temperature condition is an important factor affecting the long-term sealing reliability of hydrogen fuel cells. The sealing performance of rubber gaskets under temperature loads is not only related to the macroscopic characteristics of the material, but also directly affected by the contact state of rough sealing interface which contains microscopic protrusions. The multi-scale contact model, which contains the morphology feature under micro-scale and the material properties under the macro-scale, for the rough sealing interface between the rubber gasket and the metal plate in hydrogen fuel cells has been established in this paper. By studying the contact state of the multi-scale model under alternating temperature loads, the interfacial leaking of fuel cells under complex temperature loads has also been modeled. The long-term sealing reliability of the multi-scale model has been verified by measuring the interfacial leakage rates of an interfacial sealing device that has withstood the high-low alternating temperature load for 21 days. It can be found through researching the contact state of sealing interface based on multi-scale method that the maximum contact stress of the rough fuel cell sealing interface increases continuously with the increase of alternating temperature cycling times, meaning in a decrease in the actual contact area and an increase in leaking channels. The sealing performance of hydrogen fuel cells decreases by 37.08% within 21 days, with a decrease of 9.62% from the 7th to the 21st day, which is closer to the measured values.