Display omitted •Radial distribution function can evaluate interaction behavior of rubber asphalt.•Agglomeration of rubber-asphalt is more obvious than inter-components of asphalt.•Adsorption of rubber to asphalt follows this order: BR > SBR > NR.•Agglomeration of rubber asphalt is more clustered for more light fractions asphalt. In order to clear the interaction mechanism between rubber and asphalt binder in rubber asphalt, radial distribution function was selected to investigate the variation of the agglomeration of rubber asphalt with rubber and asphalt binder types, where molecular models of rubber asphalt were built firstly, molecular dynamics simulations were performed afterwards and the variation of agglomeration behavior and adsorption effect were analyzed finally based on Materials Studio 8.0. The results show that the agglomeration of asphalt binder is changed significantly with the addition of rubber. The agglomerations of rubber-naphthene aromatic and rubber-saturate is more clustered than that of asphaltene-naphthene aromatic and asphaltene-saturate, and the agglomeration of rubber-naphthene aromatic is more clustered than that of rubber-saturate. The adsorption of different rubber types to light fractions of asphalt binder follows this order: cis-polybutadiene rubber (BR) > styrene butadiene rubber (SBR) > natural rubber (NR). In addition, the more clustered agglomeration structure of rubber-asphalt will be formed with the higher proportion of naphthene aromatic and saturate in asphalt binder.