Flow accelerated corrosion (FAC) is the main failure cause of the secondary circuit carbon steel piping in nuclear power plants. The piping failures caused by FAC have resulted in numerous unplanned outages and tragic fatalities. The existing researches focus on the main factors contributing to FAC, which include metallurgical factors, environmental factors and hydrodynamic factors. Some effective FAC management methods and programs with long term monitoring and inspection data analysis are recommended. But a comprehensive FAC management system should be developed in order to mitigate and manage FAC systematically. In this paper, the FAC influencing factors are analyzed in combination with the operating conditions of the secondary circuit piping in the Third Qinshan Nuclear Power Plant(TQNPP), China (Third Qinshan Nuclear Power Company Limited, China). A comprehensive FAC mitigation and management system is developed for TQNPP secondary circuit piping. The system is composed of five processes, viz. Materials substitution, water chemical optimization, long-term monitor strategy for the susceptible piping, integrity evaluation of the local thinning defects, and repair or replacement. With the implementation of the five processes, the material of FAC sensitive pipe fittings are modified from carbon steel to stainless steel, N2H4 and NH3 are finally selected as the water chemical regulator of secondary circuit, the secondary circuit pips are classified according to FAC susceptibility in order to conduct long term monitoring strategy, and an integrity evaluation flow for local thinning caused by FAC in carbon steel piping is developed. If the component with local thinning defects is not fit-for-service, corresponding repair or replacement should be conducted. The comprehensive FAC mitigation and management system with five interrelated processes would be a cost-effective method of increasing personnel safety, plant safety and availability.