A method for controlling an exhaust gas purification system that can effectively implement desulfation of a selective catalytic reduction (SCR) device. The method for controlling an exhaust gas purification system, in which a diesel particulate filter (DPF) and an SCR device are combined, may include calculating a sulfur poisoning amount of the SCR device and an amount of soot loading in the DPF; and increasing a temperature of the SCR device to a desulfation temperature when the sulfur poisoning amount is greater than a first predetermined value and the amount of soot loading is less than a second predetermined value.