A three-dimensional modified discrete element method in which the hydrodynamic drag force and static interparticle force are taken into account is proposed to simulate the deformation process of two types of large aggregates depositing to a plate in a viscous fluid under Various external forces. It is found that the changes of the structure and the average cross-section density of aggregates in the deformation process look reasonable, and the following microscopic features are predicted. (1) When the aggregate is not destroyed completely by the external force, the portions of high density appear not only at the bottom but also at the position a little lower from the top. (2) When the aggregate is destroyed completely by the external force, the final aggregate is composed of at least two structures; the highly compacted structure just above the plate and the much less compacted structure above it. (3) The density of an aggregate is able to be increased by applying an external force weak enough for particles to rearrange themselves to form the compact structure. (4) The unevenness of the density distribution in an aggregate of loose structure will be increased during the deformation, because each portion of different density in the aggregate will sediment at a different velocity.