- Protein folding conformations take the form of networks, sets of conformations (vertices) joined together in pairs by links or edges. Protein folding conformation network is a complex network, and has scale-free property that many networks have in common. Understanding the scale-free property in the network of protein folding conformation, one can find the better conformation of protein folding which closes to nature. This paper constructs a complex network of protein folding conformation and analyzes its small world and scale-free properties in the network of protein folding conformation in order to study evolving process of protein structure and predict protein structure.