Currently, the development of flood control system of Nanjing City has been entering a new critical phase, facing some great challenging problems that never experienced before. To meet these challenges, this research initially reviewed the developing process of flood control system of Nanjing City after China's reform and opening up. Based on the analysis of current flood control situation, four major challenge of was summarized. To solve these problems, this research provided some productive suggestions for future development of flood control system of Nanjing City from six perspectives, namely principle of flood control, layout of flood control system, drainage system improvement, flood management, technology application and supporting measures.