As their characteristic dimensions are reduced to the nanoscale regime, such as single layer and single atom, the materials exhibit novel physical and chemical properties. Both the two-dimensional materials and the ordered array of single atoms or molecules 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 fabricating the ordered array of single atoms or molecules. Using in-situ silicene preparation, molecular deposition, ultra-high vacuum scanning tunneling microscope (STM), and scanning tunneling spectroscopy (STS), the electronic structures, surface work functions and adsorption behaviors of CoPc molecules on three silicene superstructures ((4 × 4), ( $\sqrt {13} \times \sqrt {13} $ ), and ( $2\sqrt 3 \times 2\sqrt 3 $ )) are studied. Firstly, the three silicene superstructures have similar electronic structures according to the characterization from the d I/d Vcurve at 77 K. The electronic structure varies on an atomic scale. With the disordering increasing, the full width at half maximum of the +0.6 V states broadens from (4 × 4) to ( $\sqrt {13} \times \sqrt {13} $ ) to ( $2\sqrt 3 \times 2\sqrt 3 $ ). Secondly, the average surface work functions of the three superstructures of silicene also vary on an atomic scale and are all higher than those on the Silver surface. So, electrons are probably transferred from the Ag substrate to the single-layer silicene. The number of the transferred electrons increases from (4 × 4) structure, ( $\sqrt {13} \times \sqrt {13} $ ) structure, to ( $2\sqrt 3 \times 2\sqrt 3 $ ) structure. Thirdly, the change of the surface work function on an atomic scale plays an important role in selectively adsorbing the CoPc molecules, which causes the symmetry of CoPc electronic structure to break. It indicates that none of the three silicene superstructures belongs 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 ones, in which there are HOMO (–0.45 V) and LUMO (+0.7 V) state. The other half has strong interaction with the silicene. The HOMO state is suppressed and there is a hybrid state at 1.0 V according to the d I/d Vcharacterization.