Polyimide (PI), due to its exceptional performance, is commonly utilized in spacecraft. However, when such polymers are used in spacecraft navigating low Earth orbit, they are exposed to atomic oxygen (AO) that can cause the polymer to decompose. A protective coating method is a more effective way to safeguard the polymer from erosion caused by AO. This study employs the molecular dynamics simulation based on the reaction force field to investigate the protective effects of various coatings, including polydimethylsiloxane (PDMS), graphene (Gr), polytetrafluoroethylene (PTFE), and the (0 0 1), (0 1 1), and (1 1 1) surfaces of SiO2. The results indicate that the protective performance of the (0 1 1) surface is superior to that of the (0 0 1) and (1 1 1) surfaces. Moreover, protective coatings are classified into three categories based on different protective mechanisms: rebound, absorption, and sacrificial. The protective effectiveness of coatings depends on their anti-AO performance and ability to combine with the substrate. Gr displays exceptional anti-AO properties and can effectively shield the substrate from AO erosion. Silicone-based coatings have a superior ability to adhere to PI substrates, and PDMS is an excellent choice for protective coatings. This paper offers guidance for the protective coating method of PIs against AO erosion.