In this presentation, I will discuss about how the first-principles computational methods (quantum mechanics and molecular dynamics simulation) can make contributions to the nanobio technology: understanding of the given nanoscale systems and design of new systems. The first part is the nanostructured polymer membranes for fuel cell technology in which the first-principles methods were used to establish understandings of the relationship between the nanostructures of material and the proton transport properties. First, the hydrated nafion membrane is discussed for the structure-property relationship, and then a new molecular architecture designed from such relationship is presented. In the second part of this presentation, I will talk about the nanoscale molecular electronics such as molecular switch showing an electromechanical switching behavior. In this part, the first-principles methods predict the probable molecular configurations of molecular electronic device and its corresponding electron transport properties. For the last part of my talk, I will present the nanostructured biomaterials such as hydrogel in which a hydrophilic polymer network confines significant amount of water. To develop a good hydrogel with desirable properties in terms of mechanical and transport properties, the molecular mechanisms for mechanical deformation and molecular diffusion are investigated using the first-principles.The bottom line of my talk is how the multiscale first-principles computational methods can work together to investigate the nanoscale systems and help design new material based on the structure-property relationship for better desirable properties.