Atmospheric and bulk deposition samples collected at Leigongshan Nature Reserve (LNR) were analyzed to explore the status, transport, and deposition of atmospheric pollution—specifically, organochlorine compounds—in the foggy mountains of southwest China. Prohibition and restriction of persistent organic pollutants in the surrounding areas has led to a decline in organochlorine pesticides and polychlorinated biphenyls (PCBs), but not hexachlorobenzene (HCB), in the air. Wet deposition is a factor that strongly influences atmospheric input at LNR. Despite their relatively low atmospheric concentration levels, heavy precipitation could increase the deposition of hexachlorocyclohexanes (HCHs) and HCB in the summer. Air HCHs exhibited a “bimodal” pattern, with higher concentrations in spring and autumn and lower concentrations in summer. The low levels in summer are achieved at the expense of high surface input into the ground along their transport routes from South and Southeast Asia to southwest China. The HCB at LNR mainly originates from mainland China. The deposition fluxes are influenced by the enhanced washout of atmospheric particles in the rainy season and elevated particle-associated content in the winter. The potential sources of o,p’-DDT, p,p’-DDT, and PCBs are distributed widely over western low-latitudinal areas and eastern China. Atmospheric transport and deposition in spring and summer contributed to a significant proportion of the annual total fluxes when the air mass arrives from Southeast Asia, increasing rainfall at LNR. The foggy local weather might also enhance this deposition, eventually leading to the accumulation of pollutants at LNR.