Vallisneria natans is one of the most common submerged macrophytes in lakes of China. In present, the growth strategies of V. natans population in the water ecological restoration project remain unclear. In this paper, the responses of V. natans morphological traits such as leaf, stolon and tuber and population parameters such as plant number, stolon number and biomass to water depth were discussed on basis of one year effects after the implementation of water ecological restoration project. The growth strategies of V. natans were also analyzed. The results showed that the plant number per area and stolon number per area significantly decreased with the increasing of water depth, whereas the above-ground biomass increased significantly. The leaf length, leaf width, leaf thickness, leaf area, stolon length, stolon diameter and tuber diameter also increased significantly with the water depth increasing. Among them, the leaf length and leaf area varied dramatically because they were sensitive to water depth, whereas leaf width, leaf thickness, stolon length and diameter, and tuber diameter varied lightly and were insensitive to water depth. A trade-off between parent shoot growth and daughter shoot output was found under stress of less light. V. natans guarantees the resource utilization efficiency of parent shoots by increasing investments to leaf. On the other hand, V. natans improves the growth of daughter shoots by decreasing the parent shoot density, and thus the plant realizes the spatial niche expansion and population regeneration. In water ecological restoration project, considering the regeneration ability of V. natans population and construction maneuverability, water depth at appropriate 0.5 m to 1.0 m is suggested.