Bottom-up technology is a bridge connecting a two-dimensional (2D) monolayer structure with a three-dimensional (3D) bulk structure. From 2D to 3D, it helps us to understand the driving force of an organization process to control the molecular arrangement in the 3D phase. Here, we aimed at the fabrication of multilayer nanostructures on solid substrates. Bis(3,5-diacidic)diazobenzene (NN4A) was chosen as one molecule because of its photosensitive azo group and carboxylic group possessing hydrogen bonding effect, while porphyrin molecules composed of different numbers and positions of carboxylic acid groups were used as the other component. It was found that the porphyrin molecules could adopt different adsorption configurations because of the influence of carboxylic groups, leading to different subsequent coassemblies on the solid surface. The NN4A/porphyrin systems underwent structural transformation when NN4A molecules were adsorbed on the highly oriented pyrolytic graphite surface with predeposited porphyrin. This work displayed an efficient method on the construction of multilayer nanostructures in the molecular surface engineering and provided a new way to construct 3D structures based on the molecular design.