Six chiral pesticides containing chiral sulfur/phosphorus atoms were separated by supercritical fluid chromatography with supercritical CO as the main mobile phase component. The effect of the chiral stationary phase, different type and concentration of modifiers, column temperature, and backpressure on the separation efficiency was investigated to obtain the appropriate separation condition. Five chiral pesticides (isofenphos-methyl, isocarbophos, flufiprole, fipronil, and ethiprole) were baseline separated under experimental conditions, while isofenphos only obtained partial separation. The Chiralpak AD-3 column showed a better chiral separation ability than others for chiral pesticides containing chiral sulfur/phosphorus atoms. When different modifiers at the same concentration were used, the retention factor of pesticides except flufiprole decreased in the order of isopropanol, ethanol, methanol; meanwhile, the retention factor of flufiprole increased in the order of isopropanol, ethanol, methanol. For a given modifier, the retention factor and resolution decreased on the whole with the increase of its concentration. The enantiomer separation of five chiral pesticides was an "enthalpy-driven" process, and the separation factor decreased as the temperature increased. The backpressure of the mobile phase had little effect on the separation factor and resolution.