No. I have never seen any example of the Knights Templar in the middle ages using the skull and crossbones as a symbol.

From the fourteenth century onwards, medieval sculptors and artists would use the skull and bones as a symbol of death, but this had no connection to the Templars.

The graveyard of the Templars' former church at Temple, Midlothian, Scotland, contains a number of fine tombs which have the symbol of the skull and crossbones. These tombs belonged to eighteenth-century Protestants, not to Templars.