Abstract: This paper tries to probe the essence and theoretical foundation of enterprise bionics with the self-organization methodology. Through comparison and analysis, the authors think that the main reasons why the enterprise is different from the organism and the enterprise ecosystem is simi-lar to natural ecosystem are the operating mechanism and the changing law of complicated system, and point out that to learn from the nature is to learn from the optimized evolution mechanism of self-organization. In addition, the applications of self-organization theory to enterprises are explored from three levels, and the bases of methodology for the new cross-disciplinary research are found further more.