The transactive response DNA-binding protein 43 (TDP-43) is associated with several diseases such as Amyotrophic lateral sclerosis (ALS) and Frontotemporal lobar degeneration (FTLD) due to pathogenic aggregations. In this work, we examined the dimer, tetramer and hexamer models built from the RRM domains of TDP-43 using molecular dynamics simulations in combination with the protein-protein docking. Our results show that the parallel β-sheet layers in the RRM1 domains in these oligomer models were formed energetically favorable, which provide the potential binding sites in the aggregation process. The closeness of the parallel β-sheet layers from small oligomer models gradually expanded to large ones through the communication of the interaction between α1/α2 helices of RRM domains, which enhanced the binding affinities and interactions in these aggregation models to further promote the aggregation. Using the repeatable-superimposing method based on the tetramer models, we propose a new aggregation mechanism of RRM domains in TDP-43 which mediates the formation of large aggregation structure with the repeated, helical and rope-like characteristics. These new insights help to understand the amyloid-like aggregation phenomena of TDP-43 protein in ALS and FTLD diseases.