A method of controlling a medical diagnostic system using a contrast medium is provided. The method includes injecting the contrast medium into a subject; obtaining an appearance image of the subject via a first camera; obtaining a temperature distribution image of the subject via a second camera; displaying a fusion image which combines the appearance image of the subject and the temperature distribution image of the subject on a screen; determining whether a side effect of the contrast medium has occurred in the subject, based on the fusion image; and selectively controlling the medical diagnostic system depending on a result of the determining.