In order to identify the effect of fill layout and water flow rate distribution on the cooling performance of cooling tower, a three-dimensional numerical model was established based on prototype of No.6 Cooling Tower in the Second Phase of Guohua Ninghai Power Plant in Zhejiang Province. Loading the mass, momentum, energy equation was computed by using user defined function. The comparision with the field measurement data proves the accuracy of the numerical calculation result. The effects of three kinds of fills and five kinds of fills layouts on cooling performance of super-large cooling tower weve compared and analyzed. It is found that compared with biphasic wave and double oblique wave, the cooling efficiency of S wave is optimal. For S wave, based on the dimensionless radius $ \check{r}$≤0.39 (inner zone), 0.39 < $ \check{r}$≤0.70 (middle zone) and 0.70 < $ \check{r}$≤1 (outer zone), the outlet water temperature of non-uniform layout 1.25-1.5-1.25 m is 0.66 K lower than the outlet water temperature of the uniform fill layout pattern 1.5 m. It is shown that the decreased fill height in inner and outer zones results in a higher air velocity and more uniform distribution of air velocity. In addition, increasing the salinity of cooling water made the outlet water temperature of three kinds of fills improve by about 2 K. It is indicated that the rise of outlet water temperature is related to the nature of seawater itself, and fill types has little impact on outlet water temperature.