Datong Lake is an important part of the water system of Dongting Lake area. The water quality of Datong Lake has deteriorated in recent years, so the local government implemented a water system connection project in order to improve its aquatic environment. We established a two dimensional hydrodynamic-water quality numerical model of the water system connection project in Datong Lake area using MIKE21. Total nitrogen and total phosphorus were selected as the water quality indicators to simulate nitrogen and phosphorus concentration changes under six connecting and scheduling schemes. Then, the ratio of water stagnation area, concentration change index, water exchange rate and improvement rate of water quality were selected to evaluate the improvement effects of the six schemes. Results show that this water system connection project can effectively improve the aquatic environment of this lake through the implementation of the water diversion and dispatching plan. The improvement effect of the Datong Lake is optimal when the flow discharge is 30 m3/s and the water level at the outlet of Datongkou is controlled at 25.48 m in the early stage of the diversion, and the flow discharge in the later stage of diversion is main tained at water level at the outlet of the Datongkou is adjusted to 25.88 in the later stage of the diversion. This research can provide a reference for improving aquatic environment of similar shallow lakes and the efficiency of water diversion by implementing a water system connection project.