The invention discloses a system and a method for heating optical pumping bubbles by using different temperatures. The system comprises a processed empty optical pumping bubble bracket, a central temperature control unit, a temperature sensor, a heater, a liquid nitrogen storage device, four pipelines, three valve groups, two nitrogen cylinders, the optical pumping bubbles and a gas source, wherein the on / off of the heater is controlled by the central temperature control unit through the status of the temperature sensor, and the temperature statuses of the two ends of each optical pumping bubble is controlled by the on / off state of the heater. According to the system and the method, the structure is simple, the control is convenient, the first temperature of the optical pumping bubbles can be equalized, and the uniformity and orderliness of the operation of self-spin-exchange optical pumping reaction of alkali metals and inert gases in the optical pumping bubbles are guaranteed.