Provided is an apparatus for controlling fluid-heating using a polymer disk, which includes: a pump for discharging fluid at a uniform flow rate; a fluid-heating module including a polymer disk to convey the fluid discharged from the pump to allow a temperature of the fluid to periodically vary; and a controller for controlling the temperature of the fluid-heating module, whereby it is possible to be adapted to a fluid device for biochemical reaction such as DNA amplification, and simply used as a disposable device, which is low cost and readily manufactured in a multiple manner.