Structure of organizations tends to affect the complexity of their behavior during the process of organizational transformation. As a result, organizations that are more complex structurally tend to transform in the environment that is more conflict-prone. We suggest that by affecting the structure of an organization during the process of organizational transformation, its behavior and conflict environment can be controlled. This paper examines the process of organizational transformation from the perspective of the complex systems theory and chaos theory. It offers insights and implications that could lead to better strategies for managing a conflict environment of organizations.