A device and a method for controlling a high side DC/DC converter (HDC) of a hybrid vehicle are provided. The switching frequency of the HDC is variably adjusted based on situations of temperatures of an inductor and an IGBT switching element, which constitute the HDC, to maintain a balance between the temperatures of the inductor and the IGBT switching element. Accordingly, temperatures of the inductor and the IGBT switching element are detected, and the switching frequency of the HDC is variably adjusted based on a situation for each temperature of each element to maintain a balance between the temperatures of the inductor and the IGBT switching element, thereby improving the utilization rate of the IGBT switching element.