Nano- and submicron particles typically exist in the form of agglomerates. The shear flow, a common local flow, plays an important role in the breakage and restructuring of agglomerates. In this work, the discrete element method (DEM) with a cohesive contact model is used to simulate the dynamic evolution of agglomerates under shear flow. The results show that the size and structure of agglomerates at a steady state are the results of competition among the shear gradient of the flow field, the surface energy and the initial structure of the agglomerates. Based on the variation of the radius of gyration (R-g) and fractal dimension (D-f) of agglomerates with time, the following three stages can be distinguished: (a) a stage dominated by stretch and breakage, (b) a stage dominated by agglomeration and densification, and (c) a stage characterized by the steady size and structure of agglomerates. With increasing shear gradient, the agglomerate fragments at the steady stage become smaller, more compact and more uniform. When the shear gradient is high, increasing the surface energy can result in larger fragments with a more compact structure. However, when the shear gradient is low, increasing the surface energy does not lead to larger fragments. The effect of initial structure on the stable size and structure of fragments disappears gradually with the increase in shear gradient. The detailed simulation results can improve the understanding and control of the size and structure of agglomerates in practical devices. (C) 2018 Elsevier B.V. All rights reserved.