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The application of waste rubber powder (WRP) for asphalt pavement could achieve the harmless and resourceful utilization of solid waste, but the storage stability of waste rubber powder modified asphalt (RA) is one of the main problems restricting its application. Existing studies have demonstrated that graphene could enhance the storage stability of RA, but graphene's size effect on the modifying effect and its corresponding mechanism are still uncertain. In this research, the effects of graphene microstructural properties (i.e., molecular size and layer number) on the storage stability of RA were investigated by storage stability testing, dynamic shear rheometry (DSR) testing and fluorescence microscopy (FM) testing, in combination with molecular dynamics simulation (MD). The experimental results indicated that graphene improved the storage stability of RA significantly, with few-layer graphene being more effective in enhancing it. MD was used to investigate the graphene size effect on RA in compatibility, intermolecular binding energy and structural stability of the system. The simulation results revealed that small-sized graphene molecules were more compatible with RA. Meanwhile, few-layer, small-sized graphene can provide higher binding energy and better enhancement of storage stability of RA. The number of graphene layers mainly influences the binding energy rather than solubility parameters. The relative concentration distribution results demonstrated that graphene facilitated the spatial distribution of asphaltenes, rubber components and light components. This research provides theoretical support for the rational selection of microstructural properties of graphene to improve the modified asphalt storage stability performance. [ABSTRACT FROM AUTHOR]