In Korean context, the innovative cities imply new towns or urban clusters in the Non Capital Regions, all of which would accommodate the relocated Capital based public organizations. The central government-initiated innovative cities have provoked pros and cons towards their effectiveness and efficacy for the balanced territorial development. From a broader prospective, this paper firstly examines the current status quo of the innovative cities. Based on their master plans, it analyzes physical and non physical factors which would exert significant impact on the innovative cities. Secondly, it pays attention to how key factors strengthen or weaken their behavioral patterns in terms of dynamic location and implementation policies of the innovative cities. Using System dynamics approaches, it sets up couples of scenarios, categorizing between supporting and opposing arguments towards the innovative cities. Lastly, after divulging systematic structure of the innovative cities, it proposes a series of practical alternatives which would contribute to minimizing unexpected side effects or unwanted social cost in the long run. In order to guarantee reinforcing structure of the innovative cities, the paper suggests that QOL (quality of life) variables, which would require continuous investment in the social infrastructure, are pivotal in achieving original goals of the innovative cities. Otherwise, the innovative cities would not be innovative per se. In the worst case, they might be degraded into the unpopular ghost towns.