Complexity theory, which relates with chaos theory, not only emphasizes nonlinearity and unpredictability, but also focuses more on the explanations of mutual-adaptation, co-evolution, dynamic interaction, and self-organization for organizational life. Complexity is defined as that zone between chaos on one side and order on the other, which is called “edge of chaos.” In the complexity zone, while systems are filled with turmoil and confusion, they still have the maximum potential to adapt, learn and grow. Utilizing this metaphor, educational organizations to some degree could be regarded as complexity systems full of contradiction and paradox, while at the same time, providing the opportunity for change and integration. The purpose of this study was therefore to apply the complexity theory to analyze changes in educational organization. By reviewing the nine propositions of complexity theory, the three frameworks of “paradox management,” “co-evolution,” and “self-organization” emerged contextually. Then, based on the three cores of interest, value and power for educational change, the three arguments of centralization vs. decentralization, professional autonomy vs. public deference, and social justice vs. excellence were deduced accordingly. Finally, putting the three arguments under the three frameworks, this paper further discussed the implications for changes in educational organization.