In this paper, a three-dimensional planetary boundary layer (PBL) numerical model for simulating the distributions of structures of mean wind and turbulence fields on complex terrain was established. The model adopted high-order moment closure scheme. The nouhydrostatic principle was employed and fine-mesh was used for high spatial resolution. An atmospheric diffusion simulation system was developed, which consists of the PBL model and a lagrangian particle random walk atmospheric diffusion model whose input was output of the PBL model. The mean wind, Reynolds stress, and turbulence flux fields have been successfully simulated under two circumstances which were in a real deeply-concave open pit mine and an ideal deeply-concave pit, and their distribution characteristics were analysed. The spread pattern of pollutants in the pit was also simulated.