Because of their exceptional properties, polyimide (PI) polymers are widely used in various types of spacecraft. However, in low Earth orbit, spacecraft using these polymers are susceptible to atomic oxygen (AO) erosion, which will cause them to lose their original performance. Covering the PI surface with a protective coating and adding fillers to the PI matrix are two traditional methods to improve the AO erosion resistance of PI. However, a single protective method does not provide a good protective effect and does not necessarily balance the relationship between the AO resistance of the composites and other properties, such as mechanical properties. The structural design of composites can perfectly solve such problems. Therefore, two kinds of AO-resistant materials based on the PI matrix are designed in this paper, one is a hybrid-filled composite with nano-silica filler and graphene filler, and the other is a double-layer coated composite based on the structural design of a traditional bulletproof vest. And the AO incidence simulation of these two types of materials was carried out using ReaxFF-based MD simulation. The results show that the mixed filling of graphene and nano-silica not only greatly improves the AO resistance of the PI matrix, but also greatly improves the tensile mechanical properties of the matrix by adjusting the appropriate mixing ratio. The structure of PI-Gr-SiO2 (The structures are PI, Gr and SiO2 from bottom up, respectively. SiO2 will be the first to take the impact of AO.) possesses excellent resistance to AO erosion, and at the end of 64 ps of AO erosion, the PI matrix did not suffer any damage. This paper provides a new idea of material structure design using the MD method, which provides a new approach to improve the AO erosion resistance of PI and is expected to design new composites adapted to a variety of extreme environments in the future.