Abstract: Functional nanostructures are the basic units of future molecular electronics devices. One of the key problems in nanoelectronics is to control effectively their self-assembling structures and then realize quantum modulation. In this paper we give a brief introduction to our recent progress in this research field over the last few years. Various strategies have been applied to control the self-assembly of molecular architectures on well-defined metal single-crystal surfaces. In addition, it is feasible to control the local spin coupling and the competition between different tunneling channels in the molecular Kondo effect by changing the molecular adsorption configuration. Thus modulation of the local spin states of one single magnetic molecule on the metal surface can be realized.