To explore the link between Sense of Embodiment (SoE) over a virtual hand and physiological regulation of skin temperature, 24 healthy participants were immersed in virtual reality through a Head Mounted Display and had their real limb temperature recorded by means of a high-sensitivity infrared camera. Participants observed a virtual right upper limb (appearing either normally, or with the hand detached from the forearm) or limb-shaped non-corporeal control objects (continuous or discontinuous wooden blocks) from a first-person perspective. Subjective ratings of SoE were collected in each observation condition, as well as temperatures of the right and left hand, wrist and forearm. The observation of these complex, body and body-related virtual scenes resulted in increased real hand temperature when compared to a baseline condition in which a 3d virtual ball was presented. Crucially, observation of non-natural appearances of the virtual limb (discontinuous limb) and limb-shaped non-corporeal objects elicited high increase in real hand temperature and low SoE. In contrast, observation of the full virtual limb caused high SoE and low temperature changes in the real hand with respect to the other conditions. Interestingly, the temperature difference across the different conditions occurred according to a topographic rule that included both hands. Our study sheds new light on the role of an external hand's visual appearance and suggests a tight link between higher-order bodily self-representations and topographic regulation of skin temperature.