The specific methods used for recovery of the aquatic ecological system in the shallow lake are proposed. This research has been done from three aspects:1) the design of the species used for the ecological recovery; 2) the design of optimization and allocation of the aquatic communities; and 3) the design of regional arrangement of the aquatic communities. On the basis of research, the pioneer plant and the species used to establish the communities are proposed. The aquatic plant allocation focuses on the emergent aquatic plant and submergent aquatic plant. Meanwhile, the regional arrangement has been done in the aquatic plant recovery area in the Caohai Lake and the east west bank of the outer lake.