Due to the limitations of experimental methods, the study on the aggregation process of nanoparticles is quite insufficient. In this paper, molecular dynamics simulations have been used to investigate the interaction of nanoparticulate Fe3O4 (3 nm and 4 nm) during the diffusion-limited aggregation process. Results show that the particle size has a significant influence on the aggregation process, and the structural analysis has been used to explore the aggregate structure of 3 nm particles. The atomic displacement vector diagram further explains the migration mechanisms of the atom at different stages. Small particles have higher potential energy which drives the surface diffusion and gives access to the formation of new bonds. The particles form a neck with an area of 2.09 nm(2). The main growth of the neck takes place in the adhesion stage (10-50 ps). As a scientific index, AN can effectively describes the degree of aggregation between particles. (C) 2020 Published by Elsevier B.V.