As materials’ characteristic dimensions reduced to the nanoscale regime, such as single layer and single atom, they exhibit novel physical and chemical properties. Both the two-dimensional materials and the ordered array of single atom or molecule have become cutting-edge research topics in the area of modern quantum devices and catalytic science. Silicene prepared on the Ag (111) substrate exhibits abundant superstructures at different substrate temperatures and coverages. These superstructures can be reliable templates for fabrication of the ordered array of single atoms or molecule. Using in-situ Silicene preparation, molecular deposition, ultra-high vacuum scanning tunneling microscope (STM), and scanning tunneling spectroscopy (STS), the electronic structures, surface work function and adsorption behavior of CoPc molecules on three Silicene superstructures ((4×4), (√13×√13), and (2√3×2√3)) are studied. Firstly, the three Silicene superstructures have similar electronic structure according to the characterization from the dI/dV curve at 77K. The electronic structures vary at atomic scale. As the disordering increasing, the full width at half maximum of the +0.6V states become wider from (4×4), (√13×√13), to (2√3×2√3). Secondly, the average surface work functions of the three superstructures of Silicene, which also varied in atomic scale, are all higher than the Silver surface. So, electrons are probably transferred from the Ag substrate to the single-layer Silicene. The amount of the electron being transferred increases from (4×4), (√13×√13), to (2√3×2√3). Thirdly, the change of the surface work function in atomic scale plays an important role in the selective adsorption of the CoPc molecules, which causes the symmetry breaking of the CoPc electronic structure. It indicates that none of the three Silicene superstructures belong to a complete π-bond system. Especially, on the (4×4) superstructure, all CoPc molecules are divided into two halves. One half is similar to the free standing one, in which there are HOMO (-0.45V) and LUMO (+0.7V) state. The other half has strong interaction with the Silicene. The HOMO state is suppressed and there is a hybrid state at 1.0V according to the dI/dV characterization.