The Temple of the Skull gets its name from a stucco skull located at the base of the middle pier. On close inspection, the skull can be seen in this photo on the pier between the large rectangular doorway and the arch.
The relief to which the Temple of the Skull owes it name is located at the foot of one of the pilasters on the facade. It probably represents a god of the underworld wearing ear ornaments in the shape of inverted ahau.
David Stuart has some fascinating speculation in his blog Maya Decipherment: Ideas on Ancient Maya Writing and Iconography where he pursues a link between the ruler Chan Bahlam and this temple. A wonderful read!