To solve the rigid constraints of water quality and water shortage on the development of economy, it is beneficial to select regions with regional, meteorological and engineering advantages to carry out fresh water resources reserve. Therefore, we should grasp the concept of strategic reserve of freshwater resources as the starting point. It can strengthen the knowledge supply of the construction of strategic reserve of freshwater resources and design for the micro-system provide the theoretical support. As one of the national strategic reserves of freshwater resources, the construction of the reserve of freshwater resources in the three Gorges Reservoir area needs to consider the effectiveness and systematization of the system construction, and accurately grasp the conceptual implication and value pursuit of the strategic reserve of freshwater resources. The practice of freshwater resources reserve shows the system construction of the strategic reserve of freshwater resources in the three Gorges Reservoir area should adopt the progressive time line map which include Legal gap period, initial period and perfect period and the diversified system tools which include command-control type, economic incentive type, public participation type.