The invention discloses a pest killing and sterilizing method and system for a warehouse. The method comprises the steps as follows: an ozone generator generates ozone, and the ozone is input into a goods pile from the bottom of the warehouse through an air intake fan; fumigation pest killing and sterilization are performed on the goods pile according to the preset ozone concentration and time; asuction fan sucks the ozone from the top of the warehouse; the ozone generator generates ozone, and the ozone is input into the goods pile from the top of the warehouse through the air intake fan; fumigation pest killing and sterilization are performed on the goods pile according to the preset ozone concentration and time; and the suction fan sucks the ozone from the bottom of the warehouse. By means of the method and the system, the problems of drug resistance of chemical fumigants for pests and pollution to food and drugs can be solved, pest killing, sterilization and pesticide residue removal can be realized, and the method and the system are green and environmentally friendly.