Control of complex systems is one of important files in complex systems, that not only relies on the essence of complex systems which is denoted by the core concept – emergence, but also embodies the elementary concept in control theory. Aiming at giving a clear and self-contained description of emergence, the paper introduces a formal way to completely describe the formation and dynamics of emergence in complex systems. Consequently, this paper indicates the Emergence-Oriented Control methodology that contains three kinds of basic control schemes: the direct control, the system re-structuring and the system calibration. As a universal ontology, the Emergence-Oriented Control provides a powerful tool for identifying and resolving control problems in specific systems., {"references":["Y. Bar-Yam, Overview: The Dynamics of Complex Systems - Examples,\nQuestions, Methods and Concepts, ser. The Advanced Book Studies in\nNonlinearity series. Addison Wesley Longman, 2002, ch. 0.","M. 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