Abstract-To explore new system self-organizing theory, it's urgent to find a new method in the system science. This paper combines factor space theory with system non-optimum theory, applies it into the research of system self-organizing theory and proposes new concepts as system factor space, object-factor and space-order relation. It constructs factor-space framework of system self-organizing based on factor mapping and object inversion, studies system ordering from a new perspective with optimum and non-optimum attributes as the basis of system uncertainty, and expands factor space theory from (0, ) fo to ( ,0) fo . The research suggests that the construction of system factor space is to build an information system capable of selflearning for system self-organization and better enhance functions of system self-organization by adopting information fusion of data analysis and perception judgment.