Molecular Simulation is a method to simulate the structure and behavior of molecules by using computer models at the atomic level, and then to simulate the various physical and chemical properties of the Molecular system. It is based on the experiment, through the basic principles, to build a set of models and algorithms, so as to calculate the reasonable molecular structure and molecular behavior. Molecular simulation can not only simulate the static structure of molecules, but also simulate the dynamic behavior of molecular systems. In this study, molecular simulation for modeling of nano-bubble and nanofilm was proposed and its application was introduced. It can be used for molecular sieve catalyst structure characterization, synthesis design, adsorption and diffusion. It can construct and characterize the structure of polymer chains and crystalline or amorphous bulk polymers, including blending behavior, mechanical properties, diffusion, cohesion and wetting, surface bonding and other important properties.