Natural draft wet cooling tower is widely used in cold end system of thermal power plants, however, the water droplets in the central area cannot be sufficiently cooled due to small air flow rate. In this paper, a novel water distribution mode is proposed for the wet cooling tower, in which the water distribution area is divided into four subdomains equally in the radius direction, with the diameters of sprayed water droplets from the inside to the outside of 4 mm, 3 mm, 1 mm and 0.5 mm, respectively. The three-dimensional numerical model of natural draft wet cooling tower is developed and validated by the published data, and the cooling performance with the novel water distribution mode is then obtained. The results show that the air velocity in the central area is significantly increased thus the velocity gets more uniformly distributed with the novel water distribution mode. Besides, the thermal performance in the external area is also improved thanks to the larger contact area between the cooling air and water droplets. By comparing the proposed water distribution with the conventional one, it can be found that the outlet water temperature decreases by up to 0.69 °C, and the tower with the proposed water distribution can achieve better heat and mass transfer performances with a lower air mass flow rate, which can be recommended in engineering applications for an ideal energy efficiency of cold end system.