Enterprise evolution theory in Chicago school,Williamson theory of organization evolution and Winter and Nelson's economic evolution theory have a common character,that is that they can be given theoretical foundational explanation based on methodology of functionalism.Darwinian and Lamarckian's natural selection mechanism and Elster's perfect functionalism explain the foundations of methodology on the theory of enterprise evolution from the beginning of explanation on teleology as functionalism: explanations on Teleology and perfect functionalism.Williamson's methodology on evolution of organizational structure doesn't adapt to explanation on perfect functionalism,and Nelson and Winter's methodology on enterprise evolution and Chicago school's selection theory are based on the foundation of typical perfect functionalism.