In the previous research, a novel embedded multi-phase optimization methodology was proposed to solve the NC-hard difficulty of self-organizing system involving the complex correlated constraints, which has been theoretically verified. This paper takes a serial of comparable experiments to demonstrate the efficiency of the previously proposed novel methodology. First, the description of the universal problem is given, based which the mathematic model for the self-organizing system is elected. Second, a detailed example that includes complex correlated relationship is suggested. Finally, the detailed experiments verify the correct of the proposed methodology, which integrates these two sub optimization problems into a searching loop to ensure the feasibility of solution and improve the searching efficiency in the complex correlated system, with the graphics, figures, and tables.