In this paper, three small-scale contrast experimental devices of solar chimney-sea desalination integrated system are set up. Through contact thermometric element and under actual weather conditions, the paper studies the performance influence of seawater depth on solar chimney-sea desalination integrated system. The result shows that too deep water layer will increase the thermal inertia of seawater, and decrease the seawater temperature and reduce the water production of integrated system. From the viewpoint of reducing the thermal inertia, shallower water layer is always much better while ensuring sufficient water for evaporation. On the other hand, the shallower of the water layer, the greater fluctuation of hot air temperature. The temperature difference between hot air currents and the environment can be ensured of being positive when the water depth surpasses certain depth. Therefore, there is an optimized depth of the water layer in the integrated system which is to be further studied.