Multiple intermolecular interactions offer a high degree of controllability of on-surface molecular assemblies. Here, two kinds of molecular networks were formed by depositing 11,11,12,12-tetrabromo-1,4,5,8-tetraaza-9,10-anthraquinodimethane derivatives with two different alkyl groups in length (C4 and C8) on clean Ag(111) surfaces under ultrahigh vacuum. The detailed structures of each network before and after the cleavage of the C-Br bonds were investigated with high-resolution scanning tunneling microscopy at low temperature. We found that the diffusion of the Br atoms by high-temperature annealing plays a role in the formation of Br-mediated self-assembly. While dissociated Br atoms interacted with alkyl groups by hydrogen bonding through C-H⋯Br contacts in both systems, the different strengths of the van der Waals interactions between the alkyl groups resulted in the formation of different structures.